diff --git a/lib/Doctrine/ORM/Tools/SchemaTool.php b/lib/Doctrine/ORM/Tools/SchemaTool.php
index b8e62739b..99e96c5ac 100644
--- a/lib/Doctrine/ORM/Tools/SchemaTool.php
+++ b/lib/Doctrine/ORM/Tools/SchemaTool.php
@@ -247,12 +247,14 @@ class SchemaTool
             }
 
             $pkColumns = array();
+
             foreach ($class->identifier as $identifierField) {
                 if (isset($class->fieldMappings[$identifierField])) {
                     $pkColumns[] = $this->quoteStrategy->getColumnName($identifierField, $class, $this->platform);
                 } elseif (isset($class->associationMappings[$identifierField])) {
                     /* @var $assoc \Doctrine\ORM\Mapping\OneToOne */
                     $assoc = $class->associationMappings[$identifierField];
+
                     foreach ($assoc['joinColumns'] as $joinColumn) {
                         $pkColumns[] = $this->quoteStrategy->getJoinColumnName($joinColumn, $class, $this->platform);
                     }
@@ -263,6 +265,17 @@ class SchemaTool
                 $table->setPrimaryKey($pkColumns);
             }
 
+            // there can be unique indexes automatically created for join column
+            // if join column is also primary key we should keep only primary key on this column
+            // so, remove indexes overruled by primary key
+            $primaryKey = $table->getIndex('primary');
+
+            foreach ($table->getIndexes() as $idxKey => $existingIndex) {
+                if ($primaryKey->overrules($existingIndex)) {
+                    $table->dropIndex($idxKey);
+                }
+            }
+
             if (isset($class->table['indexes'])) {
                 foreach ($class->table['indexes'] as $indexName => $indexData) {
                     if( ! isset($indexData['flags'])) {
diff --git a/tests/Doctrine/Tests/ORM/Tools/SchemaToolTest.php b/tests/Doctrine/Tests/ORM/Tools/SchemaToolTest.php
index 2bd9916ce..fd2cd20f7 100644
--- a/tests/Doctrine/Tests/ORM/Tools/SchemaToolTest.php
+++ b/tests/Doctrine/Tests/ORM/Tools/SchemaToolTest.php
@@ -122,10 +122,9 @@ class SchemaToolTest extends \Doctrine\Tests\OrmTestCase
      */
     public function testSchemaHasProperIndexesFromUniqueConstraintAnnotation()
     {
-        $em = $this->_getTestEntityManager();
+        $em         = $this->_getTestEntityManager();
         $schemaTool = new SchemaTool($em);
-
-        $classes = [
+        $classes    = [
             $em->getClassMetadata(__NAMESPACE__ . '\\UniqueConstraintAnnotationModel'),
         ];
 
@@ -138,6 +137,25 @@ class SchemaToolTest extends \Doctrine\Tests\OrmTestCase
         $this->assertTrue($table->hasIndex('primary'));
         $this->assertTrue($table->hasIndex('uniq_hash'));
     }
+
+    public function testRemoveUniqueIndexOverruledByPrimaryKey()
+    {
+        $em         = $this->_getTestEntityManager();
+        $schemaTool = new SchemaTool($em);
+        $classes    = [
+            $em->getClassMetadata(__NAMESPACE__ . '\\FirstEntity'),
+            $em->getClassMetadata(__NAMESPACE__ . '\\SecondEntity')
+        ];
+
+        $schema = $schemaTool->getSchemaFromMetadata($classes);
+
+        $this->assertTrue($schema->hasTable('first_entity'), "Table first_entity should exist.");
+
+        $indexes = $schema->getTable('first_entity')->getIndexes();
+
+        $this->assertCount(1, $indexes, "there should be only one index");
+        $this->assertTrue(current($indexes)->isPrimary(), "index should be primary");
+    }
 }
 
 /**
@@ -187,3 +205,45 @@ class UniqueConstraintAnnotationModel
      */
     private $hash;
 }
+
+/**
+ * @Entity
+ * @Table(name="first_entity")
+ */
+class FirstEntity
+{
+    /**
+     * @Id
+     * @Column(name="id")
+     */
+    public $id;
+
+    /**
+     * @OneToOne(targetEntity="SecondEntity")
+     * @JoinColumn(name="id", referencedColumnName="fist_entity_id")
+     */
+    public $secondEntity;
+
+    /**
+     * @Column(name="name")
+     */
+    public $name;
+}
+
+/**
+ * @Entity
+ * @Table(name="second_entity")
+ */
+class SecondEntity
+{
+    /**
+     * @Id
+     * @Column(name="fist_entity_id")
+     */
+    public $fist_entity_id;
+
+    /**
+     * @Column(name="name")
+     */
+    public $name;
+}
\ No newline at end of file