diff --git a/framework/CHANGELOG.md b/framework/CHANGELOG.md
index 037e90ec2a..b37d039ee8 100644
--- a/framework/CHANGELOG.md
+++ b/framework/CHANGELOG.md
@@ -36,7 +36,7 @@ Yii Framework 2 Change Log
 - Enh #12881: Added `removeValue` method to `yii\helpers\BaseArrayHelper` (nilsburg)
 - Enh #12901: Added `getDefaultHelpHeader` method to the `yii\console\controllers\HelpController` class to be able to override default help header in a class heir (diezztsk)
 - Enh: Added constants for specifying `yii\validators\CompareValidator::$type` (cebe)
-- Bug #12974: Changed order of migrations history in `yii\console\controllers\MigrateController::getMigrationHistory()` (evgen-d)
+- Bug #12974: Fixed incorrect order of migrations history in case `yii\console\controllers\MigrateController::$migrationNamespaces` is in use (evgen-d, klimov-paul)
 
 
 2.0.10 October 20, 2016
diff --git a/framework/console/controllers/MigrateController.php b/framework/console/controllers/MigrateController.php
index 58941a3b3c..a91c6220ef 100644
--- a/framework/console/controllers/MigrateController.php
+++ b/framework/console/controllers/MigrateController.php
@@ -199,27 +199,48 @@ class MigrateController extends BaseMigrateController
         if ($this->db->schema->getTableSchema($this->migrationTable, true) === null) {
             $this->createMigrationHistoryTable();
         }
-        $query = new Query;
-        $rows = $query->select(['version', 'apply_time'])
+        $query = (new Query())
+            ->select(['version', 'apply_time'])
             ->from($this->migrationTable)
-            ->orderBy('apply_time DESC, version DESC')
-            ->limit($limit)
-            ->createCommand($this->db)
-            ->queryAll();
+            ->orderBy(['apply_time' => SORT_DESC, 'version' => SORT_DESC]);
+
+        if (empty($this->migrationNamespaces)) {
+            $query->limit($limit);
+            $rows = $query->all($this->db);
+            $history = ArrayHelper::map($rows, 'version', 'apply_time');
+            unset($history[self::BASE_MIGRATION]);
+            return $history;
+        }
+
+        $rows = $query->all($this->db);
+
         $history = [];
-        foreach ($rows as $row) {
+        foreach ($rows as $key => $row) {
             if ($row['version'] === self::BASE_MIGRATION) {
                 continue;
             }
             if (preg_match('/m?(\d{6}_?\d{6})(\D.*)?$/is', $row['version'], $matches)) {
                 $time = str_replace('_', '', $matches[1]);
-                $history['m' . $time . $matches[2]] = $row;
+                $row['canonicalVersion'] = $time;
+            } else {
+                $row['canonicalVersion'] = $row['version'];
             }
+            $row['apply_time'] = (int)$row['apply_time'];
+            $history[] = $row;
         }
-        // sort history in desc order
-        uksort($history, function ($a, $b) {
-            return strcasecmp($b, $a);
+
+        usort($history, function ($a, $b) {
+            if ($a['apply_time'] === $b['apply_time']) {
+                if (($compareResult = strcasecmp($b['canonicalVersion'], $a['canonicalVersion'])) !== 0) {
+                    return $compareResult;
+                }
+                return strcasecmp($b['version'], $a['version']);
+            }
+            return ($a['apply_time'] > $b['apply_time']) ? -1 : +1;
         });
+
+        $history = array_slice($history, 0, $limit);
+
         $history = ArrayHelper::map($history, 'version', 'apply_time');
 
         return $history;
diff --git a/tests/framework/console/controllers/MigrateControllerTest.php b/tests/framework/console/controllers/MigrateControllerTest.php
index 1dbf4d4ae8..c22cd74733 100644
--- a/tests/framework/console/controllers/MigrateControllerTest.php
+++ b/tests/framework/console/controllers/MigrateControllerTest.php
@@ -218,4 +218,60 @@ class MigrateControllerTest extends TestCase
             $this->assertCommandCreatedFile('junction_test', $migrationName, 'post_tag');
         }
     }
+
+    /**
+     * @see https://github.com/yiisoft/yii2/issues/12980
+     */
+    public function testGetMigrationHistory()
+    {
+        $controllerConfig = [
+            'migrationPath' => null,
+            'migrationNamespaces' => [$this->migrationNamespace]
+        ];
+        $this->runMigrateControllerAction('history', [], $controllerConfig);
+
+        $controller = $this->createMigrateController($controllerConfig);
+        $controller->db = Yii::$app->db;
+
+        Yii::$app->db->createCommand()
+            ->batchInsert(
+                'migration',
+                ['version', 'apply_time'],
+                [
+                    ['app\migrations\M140506102106One', 10],
+                    ['app\migrations\M160909083544Two', 10],
+                    ['app\modules\foo\migrations\M161018124749Three', 10],
+                    ['app\migrations\M160930135248Four', 20],
+                    ['app\modules\foo\migrations\M161025123028Five', 20],
+                    ['app\migrations\M161110133341Six', 20],
+                ]
+            )
+            ->execute();
+
+        $rows = $this->invokeMethod($controller, 'getMigrationHistory', [10]);
+
+        $this->assertSame(
+            [
+                'app\migrations\M161110133341Six',
+                'app\modules\foo\migrations\M161025123028Five',
+                'app\migrations\M160930135248Four',
+                'app\modules\foo\migrations\M161018124749Three',
+                'app\migrations\M160909083544Two',
+                'app\migrations\M140506102106One',
+            ],
+            array_keys($rows)
+        );
+
+        $rows = $this->invokeMethod($controller, 'getMigrationHistory', [4]);
+
+        $this->assertSame(
+            [
+                'app\migrations\M161110133341Six',
+                'app\modules\foo\migrations\M161025123028Five',
+                'app\migrations\M160930135248Four',
+                'app\modules\foo\migrations\M161018124749Three',
+            ],
+            array_keys($rows)
+        );
+    }
 }
\ No newline at end of file