diff --git a/src/applications/diffusion/query/DiffusionCommitQuery.php b/src/applications/diffusion/query/DiffusionCommitQuery.php
--- a/src/applications/diffusion/query/DiffusionCommitQuery.php
+++ b/src/applications/diffusion/query/DiffusionCommitQuery.php
@@ -183,6 +183,9 @@
       ->withIDs($repository_ids)
       ->execute();
 
+    $min_qualified = PhabricatorRepository::MINIMUM_QUALIFIED_HASH;
+    $result = array();
+
     foreach ($commits as $key => $commit) {
       $repo = idx($repos, $commit->getRepositoryID());
       if ($repo) {
@@ -190,36 +193,40 @@
       } else {
         unset($commits[$key]);
       }
-    }
-
-    if ($this->identifiers !== null) {
-      $ids = array_fuse($this->identifiers);
-      $min_qualified = PhabricatorRepository::MINIMUM_QUALIFIED_HASH;
 
-      $result = array();
-      foreach ($commits as $commit) {
-        $prefix = 'r'.$commit->getRepository()->getCallsign();
+      // Build the identifierMap
+      if ($this->identifiers !== null) {
+        $ids = array_fuse($this->identifiers);
+        $prefixes = array(
+          'r'.$commit->getRepository()->getCallsign(),
+          'r'.$commit->getRepository()->getCallsign().':',
+          'r'.$commit->getRepository()->getID().':',
+          '', // No prefix is valid too and will only match the commitIdentifier
+        );
         $suffix = $commit->getCommitIdentifier();
 
         if ($commit->getRepository()->isSVN()) {
-          if (isset($ids[$prefix.$suffix])) {
-            $result[$prefix.$suffix][] = $commit;
+          foreach ($prefixes as $prefix) {
+            if (isset($ids[$prefix.$suffix])) {
+              $result[$prefix.$suffix][] = $commit;
+            }
           }
         } else {
           // This awkward construction is so we can link the commits up in O(N)
           // time instead of O(N^2).
           for ($ii = $min_qualified; $ii <= strlen($suffix); $ii++) {
             $part = substr($suffix, 0, $ii);
-            if (isset($ids[$prefix.$part])) {
-              $result[$prefix.$part][] = $commit;
-            }
-            if (isset($ids[$part])) {
-              $result[$part][] = $commit;
+            foreach ($prefixes as $prefix) {
+              if (isset($ids[$prefix.$part])) {
+                $result[$prefix.$part][] = $commit;
+              }
             }
           }
         }
       }
+    }
 
+    if ($result) {
       foreach ($result as $identifier => $matching_commits) {
         if (count($matching_commits) == 1) {
           $result[$identifier] = head($matching_commits);
@@ -229,7 +236,6 @@
           unset($result[$identifier]);
         }
       }
-
       $this->identifierMap += $result;
     }
 
@@ -327,9 +333,9 @@
       $bare = array();
       foreach ($this->identifiers as $identifier) {
         $matches = null;
-        preg_match('/^(?:r([A-Z]+))?(.*)$/', $identifier, $matches);
-        $repo = nonempty($matches[1], null);
-        $identifier = nonempty($matches[2], null);
+        preg_match('/^(?:r([A-Z]+:?|[0-9]+:))?(.*)$/', $identifier, $matches);
+        $repo = nonempty(rtrim($matches[1], ':'), null);
+        $commitIdentifier = nonempty($matches[2], null);
 
         if ($repo === null) {
           if ($this->defaultRepository) {
@@ -338,14 +344,14 @@
         }
 
         if ($repo === null) {
-          if (strlen($identifier) < $min_unqualified) {
+          if (strlen($commitIdentifier) < $min_unqualified) {
             continue;
           }
-          $bare[] = $identifier;
+          $bare[] = $commitIdentifier;
         } else {
           $refs[] = array(
             'callsign' => $repo,
-            'identifier' => $identifier,
+            'identifier' => $commitIdentifier,
           );
         }
       }
@@ -362,14 +368,17 @@
 
       if ($refs) {
         $callsigns = ipull($refs, 'callsign');
+
         $repos = id(new PhabricatorRepositoryQuery())
           ->setViewer($this->getViewer())
-          ->withCallsigns($callsigns)
-          ->execute();
-        $repos = mpull($repos, null, 'getCallsign');
+          ->withIdentifiers($callsigns);
+        $repos->execute();
+
+        $repos = $repos->getIdentifierMap();
 
         foreach ($refs as $key => $ref) {
           $repo = idx($repos, $ref['callsign']);
+
           if (!$repo) {
             continue;
           }
diff --git a/src/applications/diffusion/remarkup/DiffusionCommitRemarkupRule.php b/src/applications/diffusion/remarkup/DiffusionCommitRemarkupRule.php
--- a/src/applications/diffusion/remarkup/DiffusionCommitRemarkupRule.php
+++ b/src/applications/diffusion/remarkup/DiffusionCommitRemarkupRule.php
@@ -22,7 +22,6 @@
       ->withIdentifiers($ids);
 
     $query->execute();
-
     return $query->getIdentifierMap();
   }
 
diff --git a/src/applications/diffusion/remarkup/DiffusionRepositoryRemarkupRule.php b/src/applications/diffusion/remarkup/DiffusionRepositoryRemarkupRule.php
--- a/src/applications/diffusion/remarkup/DiffusionRepositoryRemarkupRule.php
+++ b/src/applications/diffusion/remarkup/DiffusionRepositoryRemarkupRule.php
@@ -8,18 +8,18 @@
   }
 
   protected function getObjectIDPattern() {
-    return '[A-Z]+';
+    return '[A-Z0-9]+';
   }
 
   protected function loadObjects(array $ids) {
     $viewer = $this->getEngine()->getConfig('viewer');
 
-    $repositories = id(new PhabricatorRepositoryQuery())
+    $repos = id(new PhabricatorRepositoryQuery())
       ->setViewer($viewer)
-      ->withCallsigns($ids)
-      ->execute();
+      ->withIdentifiers($ids);
 
-    return mpull($repositories, null, 'getCallsign');
+    $repos->execute();
+    return $repos->getIdentifierMap();
   }
 
 }
diff --git a/src/applications/repository/phid/PhabricatorRepositoryCommitPHIDType.php b/src/applications/repository/phid/PhabricatorRepositoryCommitPHIDType.php
--- a/src/applications/repository/phid/PhabricatorRepositoryCommitPHIDType.php
+++ b/src/applications/repository/phid/PhabricatorRepositoryCommitPHIDType.php
@@ -54,9 +54,9 @@
     $min_qualified   = PhabricatorRepository::MINIMUM_QUALIFIED_HASH;
 
     return
-      'r[A-Z]+[1-9]\d*'.
+      'r([A-Z]+:?|[0-9]+:)[1-9]\d*'.
       '|'.
-      'r[A-Z]+[a-f0-9]{'.$min_qualified.',40}'.
+      'r([A-Z]+:?|[0-9]+:)[a-f0-9]{'.$min_qualified.',40}'.
       '|'.
       '[a-f0-9]{'.$min_unqualified.',40}';
   }
diff --git a/src/applications/repository/phid/PhabricatorRepositoryRepositoryPHIDType.php b/src/applications/repository/phid/PhabricatorRepositoryRepositoryPHIDType.php
--- a/src/applications/repository/phid/PhabricatorRepositoryRepositoryPHIDType.php
+++ b/src/applications/repository/phid/PhabricatorRepositoryRepositoryPHIDType.php
@@ -44,33 +44,19 @@
   }
 
   public function canLoadNamedObject($name) {
-    return preg_match('/^r[A-Z]+$/', $name);
+    return preg_match('/^r[A-Z0-9]+$/', $name);
   }
 
   public function loadNamedObjects(
     PhabricatorObjectQuery $query,
     array $names) {
 
-    $id_map = array();
-    foreach ($names as $name) {
-      $id = substr($name, 1);
-      $id_map[$id][] = $name;
-    }
-
-    $objects = id(new PhabricatorRepositoryQuery())
+    $results = id(new PhabricatorRepositoryQuery())
       ->setViewer($query->getViewer())
-      ->withCallsigns(array_keys($id_map))
-      ->execute();
-
-    $results = array();
-    foreach ($objects as $object) {
-      $callsign = $object->getCallsign();
-      foreach (idx($id_map, $callsign, array()) as $name) {
-        $results[$name] = $object;
-      }
-    }
+      ->withIdentifiers($names);
+    $results->execute();
 
-    return $results;
+    return $results->getIdentifierMap();
   }
 
 }
diff --git a/src/applications/repository/query/PhabricatorRepositoryQuery.php b/src/applications/repository/query/PhabricatorRepositoryQuery.php
--- a/src/applications/repository/query/PhabricatorRepositoryQuery.php
+++ b/src/applications/repository/query/PhabricatorRepositoryQuery.php
@@ -12,6 +12,9 @@
   private $remoteURIs;
   private $anyProjectPHIDs;
 
+  private $identifierMap;
+  private $allowMultipleIDTypes = false;
+
   const STATUS_OPEN = 'status-open';
   const STATUS_CLOSED = 'status-closed';
   const STATUS_ALL = 'status-all';
@@ -47,6 +50,27 @@
     return $this;
   }
 
+  public function withIdentifiers(array $identifiers) {
+    $this->allowMultipleIDTypes = true;
+    $ids = array(); $callsigns = array();
+    foreach ($identifiers as $identifier) {
+      // Strip the leading lowercase 'r' in the repo identifier if present
+      if ($identifier[0] == 'r') {
+        $identifier = substr($identifier, 1);
+      }
+
+      if (ctype_digit($identifier)) {
+        $ids[$identifier] = $identifier;
+      } else {
+        // FIXME: Find out how to identify PHIDs and handle them here too
+        $callsigns[$identifier] = $identifier;
+      }
+    }
+    $this->ids = $ids;
+    $this->callsigns = $callsigns;
+    return $this;
+  }
+
   public function withStatus($status) {
     $this->status = $status;
     return $this;
@@ -102,6 +126,14 @@
     return $this;
   }
 
+  public function getIdentifierMap() {
+    if ($this->identifierMap === null) {
+      throw new Exception(
+        'You must execute() the query before accessing the identifier map.');
+    }
+    return $this->identifierMap;
+  }
+
   protected function loadPage() {
     $table = new PhabricatorRepository();
     $conn_r = $table->establishConnection('r');
@@ -202,6 +234,37 @@
       }
     }
 
+    // Build the identifierMap
+    $this->identifierMap = array();
+
+    if ($this->ids) {
+      foreach ($this->ids as $id) {
+        if (isset($repositories[$id])) {
+          $this->identifierMap[$id] = $repositories[$id];
+        }
+      }
+    }
+
+    if ($this->callsigns) {
+      $repository_callsigns = mpull($repositories, null, 'getCallsign');
+
+      foreach ($this->callsigns as $callsign) {
+        if (isset($repository_callsigns[$callsign])) {
+          $this->identifierMap[$callsign] = $repository_callsigns[$callsign];
+        }
+      }
+    }
+
+    if ($this->phids) {
+      $repository_phids = mpull($repositories, null, 'getPHID');
+
+      foreach ($this->phids as $phid) {
+        if (isset($repository_phids[$phid])) {
+          $this->identifierMap[$phid] = $repository_phids[$phid];
+        }
+      }
+    }
+
     return $repositories;
   }
 
@@ -387,6 +450,12 @@
         $this->callsigns);
     }
 
+    if ($this->allowMultipleIDTypes) {
+      // Connect all the existing where conditions with an OR
+      // Make sure not to insert any other where conditions above this!
+      $where = array('('.implode(' OR ', $where).')');
+    }
+
     if ($this->types) {
       $where[] = qsprintf(
         $conn_r,
@@ -420,7 +489,6 @@
     return $this->formatWhereClause($where);
   }
 
-
   public function getQueryApplicationClass() {
     return 'PhabricatorDiffusionApplication';
   }