diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4939d98a..356dc34f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@
   `migrate:create` commands: remove redundant messages, replace `>>>` with cleaner output, and move "Database
   connection" info to the top (@samdark, @vjik)
 - Enh #333: Use `newMigrationPath` and `newMigrationNamespace` as source (@Tigrov)
+- Bug #341: Fix migration namespaces and paths (@Tigrov)
 
 ## 2.0.1 December 20, 2025
 
diff --git a/composer.json b/composer.json
index 16c29a96..2aa34df0 100644
--- a/composer.json
+++ b/composer.json
@@ -90,6 +90,7 @@
         "check-dependencies": "composer-require-checker",
         "mutation": "infection",
         "psalm": "psalm",
-        "test": "phpunit --testdox --no-interaction"
+        "test": "phpunit --testdox --no-interaction",
+        "cs-fix": "php-cs-fixer fix"
     }
 }
diff --git a/src/Command/CreateCommand.php b/src/Command/CreateCommand.php
index 1ea1b4ad..1e57e263 100644
--- a/src/Command/CreateCommand.php
+++ b/src/Command/CreateCommand.php
@@ -4,6 +4,7 @@
 
 namespace Yiisoft\Db\Migration\Command;
 
+use LogicException;
 use Symfony\Component\Console\Attribute\AsCommand;
 use Symfony\Component\Console\Command\Command;
 use Symfony\Component\Console\Input\InputArgument;
@@ -150,10 +151,16 @@ protected function execute(InputInterface $input, OutputInterface $output): int
             return Command::INVALID;
         }
 
-        $migrationPath = $this->migrationService->findMigrationPath();
+        try {
+            $migrationPath = $this->migrationService->findMigrationPath();
+        } catch (LogicException $e) {
+            $io->error($e->getMessage());
+
+            return Command::INVALID;
+        }
 
         if (!is_dir($migrationPath)) {
-            $io->error("Invalid path directory $migrationPath");
+            $io->error("Invalid path directory \"$migrationPath\"");
 
             return Command::INVALID;
         }
diff --git a/src/Service/MigrationService.php b/src/Service/MigrationService.php
index 52383451..7be8fbc7 100644
--- a/src/Service/MigrationService.php
+++ b/src/Service/MigrationService.php
@@ -16,9 +16,12 @@
 use Yiisoft\Db\Migration\Migrator;
 use Yiisoft\Db\Migration\RevertibleMigrationInterface;
 
+use function array_keys;
 use function array_map;
+use function array_merge;
 use function array_unique;
 use function array_values;
+use function class_exists;
 use function closedir;
 use function dirname;
 use function gmdate;
@@ -33,6 +36,7 @@
 use function readdir;
 use function realpath;
 use function reset;
+use function rtrim;
 use function str_contains;
 use function str_replace;
 use function str_starts_with;
@@ -128,40 +132,8 @@ public function getNewMigrations(): array
             $applied[trim($class, '\\')] = true;
         }
 
-        $migrations = [];
-        $migrationPaths = $this->findSourcePaths();
-
-        foreach ($migrationPaths as [$sourcePath, $namespace]) {
-            if (!is_dir($sourcePath)) {
-                continue;
-            }
-
-            /** @var resource $handle */
-            $handle = opendir($sourcePath);
-            while (($file = readdir($handle)) !== false) {
-                if ($file === '.' || $file === '..') {
-                    continue;
-                }
-
-                $path = $sourcePath . DIRECTORY_SEPARATOR . $file;
-
-                if (is_file($path) && preg_match('/^(M(\d{12}).*)\.php$/s', $file, $matches)) {
-                    [, $class, $time] = $matches;
-
-                    if (!empty($namespace)) {
-                        $class = $namespace . '\\' . $class;
-                    }
-
-                    /** @psalm-var class-string $class */
-
-                    if (!isset($applied[$class])) {
-                        $migrations[$time . '\\' . $class] = $class;
-                    }
-                }
-            }
-            closedir($handle);
-        }
-
+        $migrations = $this->loadMigrationClasses();
+        $migrations = array_filter($migrations, static fn(string $class): bool => !isset($applied[$class]));
         ksort($migrations);
         return array_values($migrations);
     }
@@ -416,28 +388,33 @@ private function makeMigrationInstance(string $class): object
     }
 
     /**
-     * Returns the migration paths with namespaces if they are specified.
+     * Returns the migration paths with namespaces.
      *
-     * @return array<array{0: string, 1: string}>
+     * @return true[][]
+     * @psalm-return array<string, array<string, true>>
      */
     private function findSourcePaths(): array
     {
         $paths = [];
 
         if ($this->newMigrationPath !== '') {
-            $paths[] = [$this->newMigrationPath, ''];
+            $newMigrationPath = $this->normalizePath($this->newMigrationPath);
+            $newMigrationNamespaces = $this->getNamespacesFromPath($newMigrationPath);
+            $paths[$newMigrationPath] = array_fill_keys($newMigrationNamespaces, true);
         } elseif ($this->newMigrationNamespace !== '') {
             $newMigrationPath = $this->getNamespacePath($this->newMigrationNamespace);
-            $paths[] = [$newMigrationPath, $this->newMigrationNamespace];
+            $paths[$newMigrationPath][$this->newMigrationNamespace] = true;
         }
 
-        foreach ($this->sourcePaths as $sourcePaths) {
-            $paths[] = [$sourcePaths, ''];
+        foreach ($this->sourcePaths as $sourcePath) {
+            $sourcePath = $this->normalizePath($sourcePath);
+            $sourceNamespaces = $this->getNamespacesFromPath($sourcePath);
+            $paths[$sourcePath] = ($paths[$sourcePath] ?? []) + array_fill_keys($sourceNamespaces, true);
         }
 
-        foreach ($this->sourceNamespaces as $namespace) {
-            $sourcePath = $this->getNamespacePath($namespace);
-            $paths[] = [$sourcePath, $namespace];
+        foreach ($this->sourceNamespaces as $sourceNamespace) {
+            $sourcePath = $this->getNamespacePath($sourceNamespace);
+            $paths[$sourcePath][$sourceNamespace] = true;
         }
 
         return $paths;
@@ -448,6 +425,8 @@ private function findSourcePaths(): array
      *
      * @param string $namespace Namespace.
      *
+     * @throws LogicException If the namespace is invalid.
+     *
      * @return string File path.
      */
     private function getNamespacePath(string $namespace): string
@@ -462,11 +441,15 @@ private function getNamespacePath(string $namespace): string
             if (str_starts_with($namespace, trim($mapNamespace, '\\'))) {
                 /** @var string $mapDirectory */
                 $mapDirectory = reset($mapDirectories);
-                return $mapDirectory . '/' . str_replace('\\', '/', substr($namespace, strlen($mapNamespace)));
+                $path = $mapDirectory . '/' . str_replace('\\', '/', substr($namespace, strlen($mapNamespace)));
+
+                if (is_dir($path)) {
+                    return $this->normalizePath($path);
+                }
             }
         }
 
-        throw new LogicException("Invalid namespace: \"$namespace\".");
+        throw new LogicException("Invalid namespace \"$namespace\"");
     }
 
     /**
@@ -475,6 +458,7 @@ private function getNamespacePath(string $namespace): string
      * @param string $path File path.
      *
      * @return string[] Namespaces.
+     * @psalm-return list<string>
      */
     private function getNamespacesFromPath(string $path): array
     {
@@ -513,7 +497,8 @@ private function getNamespacesFromPath(string $path): array
 
         krsort($namespaces);
 
-        return array_values(reset($namespaces));
+        /** @psalm-var list<string> */
+        return array_values(array_unique(array_merge(...$namespaces)));
     }
 
     private function getVendorDir(): string
@@ -521,4 +506,73 @@ private function getVendorDir(): string
         $class = new ReflectionClass(ClassLoader::class);
         return dirname($class->getFileName(), 2);
     }
+
+    /**
+     * Loads migration classes.
+     *
+     * @return string[] List of migration classes indexed by their time stamp and file path.
+     * @psalm-return class-string[]
+     */
+    private function loadMigrationClasses(): array
+    {
+        $migrationPaths = $this->findSourcePaths();
+
+        $migrations = [];
+
+        foreach ($migrationPaths as $path => $namespaces) {
+            /** @var resource $handle */
+            $handle = opendir($path);
+            while (($file = readdir($handle)) !== false) {
+                if ($file === '.' || $file === '..') {
+                    continue;
+                }
+
+                $filePath = "$path/$file";
+
+                if (!is_file($filePath)) {
+                    continue;
+                }
+
+                if (preg_match('/^(M(\d{12}).*)\.php$/s', $file, $matches) !== 1) {
+                    continue;
+                }
+
+                [, $class, $time] = $matches;
+
+                $sortKey = "$time/$filePath";
+
+                if (isset($migrations[$sortKey])) {
+                    continue;
+                }
+
+                require_once $filePath;
+
+                foreach (array_keys($namespaces) as $namespace) {
+                    if (class_exists($namespace . '\\' . $class, false)) {
+                        /** @psalm-var class-string */
+                        $migrations[$sortKey] = $namespace . '\\' . $class;
+                        break;
+                    }
+
+                    if (class_exists($class, false)) {
+                        /** @psalm-var class-string $class */
+                        $migrations[$sortKey] = $class;
+                        break;
+                    }
+                }
+            }
+            closedir($handle);
+        }
+
+        return $migrations;
+    }
+
+    private function normalizePath(string $path): string
+    {
+        if (!is_dir($path)) {
+            throw new LogicException("Invalid path directory \"$path\"");
+        }
+
+        return rtrim(str_replace('\\', '/', $path), '/');
+    }
 }
diff --git a/tests/Common/Command/AbstractCreateCommandTest.php b/tests/Common/Command/AbstractCreateCommandTest.php
index 5a4ac47b..b6d12d24 100644
--- a/tests/Common/Command/AbstractCreateCommandTest.php
+++ b/tests/Common/Command/AbstractCreateCommandTest.php
@@ -1025,7 +1025,7 @@ public function testIncorrectNewMigrationNamespace(): void
         $output = preg_replace('/(\R|\s)+/', ' ', $command->getDisplay(true));
 
         $this->assertSame(Command::INVALID, $exitCode);
-        $this->assertStringContainsString('Invalid path directory', $output);
+        $this->assertStringContainsString('Invalid namespace "Yiisoft\Db\Migration\TestsRuntime\NotExists"', $output);
     }
 
     public function testWithoutNewMigrationNamespace(): void
diff --git a/tests/Common/Service/AbstractMigrationServiceTest.php b/tests/Common/Service/AbstractMigrationServiceTest.php
index e2e53f88..30b4d7b7 100644
--- a/tests/Common/Service/AbstractMigrationServiceTest.php
+++ b/tests/Common/Service/AbstractMigrationServiceTest.php
@@ -4,11 +4,11 @@
 
 namespace Yiisoft\Db\Migration\Tests\Common\Service;
 
+use LogicException;
 use PHPUnit\Framework\Attributes\DataProvider;
 use PHPUnit\Framework\TestCase;
 use Psr\Container\ContainerInterface;
 use ReflectionMethod;
-use Yiisoft\Db\Migration\Migrator;
 use Yiisoft\Db\Migration\Service\MigrationService;
 use Yiisoft\Db\Migration\Tests\Support\Helper\MigrationHelper;
 
@@ -28,24 +28,6 @@ public function testVersion(): void
     public function testGetNewMigrationsWithNotExistNamespace(): void
     {
         MigrationHelper::useMigrationsNamespace($this->container);
-
-        $className = MigrationHelper::createMigration(
-            $this->container,
-            'Create_Post',
-            'table',
-            'post',
-            ['name:string(50)'],
-        );
-        $this->container->get(Migrator::class)->up(new $className());
-
-        $className = MigrationHelper::createMigration(
-            $this->container,
-            'Create_User',
-            'table',
-            'user',
-            ['name:string(32)'],
-        );
-
         $service = $this->container->get(MigrationService::class);
 
         $service->setSourceNamespaces([
@@ -53,9 +35,10 @@ public function testGetNewMigrationsWithNotExistNamespace(): void
             'Yiisoft\\Db\\Migration\\TestsRuntime\\NotExists',
         ]);
 
-        $migrations = $service->getNewMigrations();
+        $this->expectException(LogicException::class);
+        $this->expectExceptionMessage('Invalid namespace "Yiisoft\Db\Migration\TestsRuntime\NotExists"');
 
-        $this->assertSame([$className], $migrations);
+        $service->getNewMigrations();
     }
 
     public static function getNewMigrationsDataProvider(): array
@@ -67,17 +50,26 @@ public static function getNewMigrationsDataProvider(): array
             'non exists newMigrationNamespace' => [
                 'expected' => [],
                 'newMigrationNamespace' => 'Yiisoft\Db\Migration\TestsRuntime\NotExists',
+                'newMigrationPath' => '',
+                'sourceNamespaces' => [],
+                'sourcePaths' => [],
+                'errorMessage' => 'Invalid namespace "Yiisoft\Db\Migration\TestsRuntime\NotExists"',
             ],
             'non exists newMigrationPath' => [
                 'expected' => [],
                 'newMigrationNamespace' => '',
                 'newMigrationPath' => dirname(__DIR__, 2) . '/non-exists-directory',
+                'sourceNamespaces' => [],
+                'sourcePaths' => [],
+                'errorMessage' => 'Invalid path directory "' . dirname(__DIR__, 2) . '/non-exists-directory"',
             ],
             'non exists sourceNamespaces' => [
                 'expected' => [],
                 'newMigrationNamespace' => '',
                 'newMigrationPath' => '',
                 'sourceNamespaces' => ['Yiisoft\Db\Migration\TestsRuntime\NotExists'],
+                'sourcePaths' => [],
+                'errorMessage' => 'Invalid namespace "Yiisoft\Db\Migration\TestsRuntime\NotExists"',
             ],
             'non exists sourcePaths' => [
                 'expected' => [],
@@ -85,13 +77,17 @@ public static function getNewMigrationsDataProvider(): array
                 'newMigrationPath' => '',
                 'sourceNamespaces' => [],
                 'sourcePaths' => [dirname(__DIR__, 2) . '/non-exists-directory'],
+                'errorMessage' => 'Invalid path directory "' . dirname(__DIR__, 2) . '/non-exists-directory"',
             ],
             'with newMigrationNamespace' => [
                 'expected' => ['Yiisoft\Db\Migration\Tests\Support\MigrationsExtra\M231108183919Empty'],
                 'newMigrationNamespace' => 'Yiisoft\Db\Migration\Tests\Support\MigrationsExtra',
             ],
             'with newMigrationPath' => [
-                'expected' => ['M231108183919Empty'],
+                'expected' => [
+                    'Yiisoft\Db\Migration\Tests\Support\MigrationsExtra\M231108183919Empty',
+                    'Yiisoft\Db\Migration\Tests\ForTest\MigrationsExtra\M231108183920DifferentNamespace',
+                ],
                 'newMigrationNamespace' => '',
                 'newMigrationPath' => dirname(__DIR__, 2) . '/Support/MigrationsExtra',
             ],
@@ -112,8 +108,8 @@ public static function getNewMigrationsDataProvider(): array
             ],
             'with different sourceNamespaces with the same path' => [
                 'expected' => [
-                    'Yiisoft\Db\Migration\Tests\ForTest\MigrationsExtra\M231108183919Empty',
                     'Yiisoft\Db\Migration\Tests\Support\MigrationsExtra\M231108183919Empty',
+                    'Yiisoft\Db\Migration\Tests\ForTest\MigrationsExtra\M231108183920DifferentNamespace',
                 ],
                 'newMigrationNamespace' => '',
                 'newMigrationPath' => '',
@@ -124,8 +120,9 @@ public static function getNewMigrationsDataProvider(): array
             ],
             'with sourcePaths with different paths' => [
                 'expected' => [
-                    'M231108183919Empty',
-                    'M231108183919Empty2',
+                    'Yiisoft\Db\Migration\Tests\Support\MigrationsExtra\M231108183919Empty',
+                    'Yiisoft\Db\Migration\Tests\Support\MigrationsExtra\M231108183919Empty2',
+                    'Yiisoft\Db\Migration\Tests\ForTest\MigrationsExtra\M231108183920DifferentNamespace',
                 ],
                 'newMigrationNamespace' => '',
                 'newMigrationPath' => '',
@@ -137,8 +134,8 @@ public static function getNewMigrationsDataProvider(): array
             ],
             'with sourceNamespaces and sourcePaths with the same path' => [
                 'expected' => [
-                    'M231108183919Empty',
                     'Yiisoft\Db\Migration\Tests\Support\MigrationsExtra\M231108183919Empty',
+                    'Yiisoft\Db\Migration\Tests\ForTest\MigrationsExtra\M231108183920DifferentNamespace',
                 ],
                 'newMigrationNamespace' => '',
                 'newMigrationPath' => '',
@@ -147,8 +144,8 @@ public static function getNewMigrationsDataProvider(): array
             ],
             'with sourceNamespaces and sourcePaths with different paths' => [
                 'expected' => [
-                    'M231108183919Empty2',
                     'Yiisoft\Db\Migration\Tests\Support\MigrationsExtra\M231108183919Empty',
+                    'Yiisoft\Db\Migration\Tests\Support\MigrationsExtra\M231108183919Empty2',
                 ],
                 'newMigrationNamespace' => '',
                 'newMigrationPath' => '',
@@ -162,7 +159,10 @@ public static function getNewMigrationsDataProvider(): array
                 'sourceNamespaces' => ['Yiisoft\Db\Migration\Tests\Support\MigrationsExtra'],
             ],
             'with newMigrationPath and sourcePaths with the same path' => [
-                'expected' => ['M231108183919Empty'],
+                'expected' => [
+                    'Yiisoft\Db\Migration\Tests\Support\MigrationsExtra\M231108183919Empty',
+                    'Yiisoft\Db\Migration\Tests\ForTest\MigrationsExtra\M231108183920DifferentNamespace',
+                ],
                 'newMigrationNamespace' => '',
                 'newMigrationPath' => dirname(__DIR__, 2) . '/Support/MigrationsExtra',
                 'sourceNamespaces' => [],
@@ -170,8 +170,8 @@ public static function getNewMigrationsDataProvider(): array
             ],
             'with newMigrationNamespace and sourcePaths with the same path' => [
                 'expected' => [
-                    'M231108183919Empty',
                     'Yiisoft\Db\Migration\Tests\Support\MigrationsExtra\M231108183919Empty',
+                    'Yiisoft\Db\Migration\Tests\ForTest\MigrationsExtra\M231108183920DifferentNamespace',
                 ],
                 'newMigrationNamespace' => 'Yiisoft\Db\Migration\Tests\Support\MigrationsExtra',
                 'newMigrationPath' => '',
@@ -192,8 +192,8 @@ public static function getNewMigrationsDataProvider(): array
             ],
             'with newMigrationPath and sourceNamespaces with different paths' => [
                 'expected' => [
-                    'M231108183919Empty2',
                     'Yiisoft\Db\Migration\Tests\Support\MigrationsExtra\M231108183919Empty',
+                    'Yiisoft\Db\Migration\Tests\Support\MigrationsExtra\M231108183919Empty2',
                 ],
                 'newMigrationNamespace' => '',
                 'newMigrationPath' => dirname(__DIR__, 2) . '/Support/MigrationsExtra2',
@@ -209,6 +209,7 @@ public function testGetNewMigrations(
         string $newMigrationPath = '',
         array $sourceNamespaces = [],
         array $sourcePaths = [],
+        string $errorMessage = '',
     ): void {
         MigrationHelper::useMigrationsNamespace($this->container);
 
@@ -218,9 +219,12 @@ public function testGetNewMigrations(
         $service->setSourceNamespaces($sourceNamespaces);
         $service->setSourcePaths($sourcePaths);
 
-        $migrations = $service->getNewMigrations();
-
-        $this->assertSame($expected, $migrations);
+        try {
+            $migrations = $service->getNewMigrations();
+            $this->assertSame($expected, $migrations);
+        } catch (LogicException $e) {
+            $this->assertSame($errorMessage, $e->getMessage());
+        }
     }
 
     public function testGetNamespacesFromPathForNoHavingNamespacePath(): void
diff --git a/tests/Migration/Service/MigrationServiceTest.php b/tests/Migration/Service/MigrationServiceTest.php
index 80ecfd0a..2a65bafd 100644
--- a/tests/Migration/Service/MigrationServiceTest.php
+++ b/tests/Migration/Service/MigrationServiceTest.php
@@ -31,7 +31,8 @@ public function testInvalidNamespace(): void
         $service->setNewMigrationNamespace('InvalidNamespace\\Hello');
 
         $this->expectException(LogicException::class);
-        $this->expectExceptionMessage('Invalid namespace: "InvalidNamespace\Hello".');
+        $this->expectExceptionMessage('Invalid namespace "InvalidNamespace\Hello"');
+
         $service->findMigrationPath();
     }
 }
diff --git a/tests/Support/MigrationsExtra/M231108183920DifferentNamespace.php b/tests/Support/MigrationsExtra/M231108183920DifferentNamespace.php
new file mode 100644
index 00000000..64e6f5b3
--- /dev/null
+++ b/tests/Support/MigrationsExtra/M231108183920DifferentNamespace.php
@@ -0,0 +1,16 @@
+<?php
+
+declare(strict_types=1);
+
+namespace Yiisoft\Db\Migration\Tests\ForTest\MigrationsExtra;
+
+use Yiisoft\Db\Migration\MigrationBuilder;
+use Yiisoft\Db\Migration\RevertibleMigrationInterface;
+use Yiisoft\Db\Migration\TransactionalMigrationInterface;
+
+final class M231108183920DifferentNamespace implements RevertibleMigrationInterface, TransactionalMigrationInterface
+{
+    public function up(MigrationBuilder $b): void {}
+
+    public function down(MigrationBuilder $b): void {}
+}