diff --git a/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py b/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
index 04345cad9a4..b03417da16f 100644
--- a/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
+++ b/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
@@ -414,6 +414,23 @@ class RepositoryDependencyInstallManager( object ):
                                     all_repo_info_dicts_keys = [ d.keys()[ 0 ] for d in all_repo_info_dicts ]
                                     if required_repo_info_dict_key not in all_repo_info_dicts_keys:
                                         all_repo_info_dicts.append( required_repo_info_dict )
+                                    else:
+                                        # required_repo_info_dict_key corresponds to the repo name.
+                                        # A single install transaction might require the installation of 2 or more repos
+                                        # with the same repo name but different owners or versions.
+                                        # Therefore, if required_repo_info_dict_key is already in all_repo_info_dicts,
+                                        # check that the tool id is already present. If it is not, we are dealing with the same repo name,
+                                        # but a different owner/changeset revision or version and we add the repo to the list of repos to be installed.
+                                        tool_id = required_repo_info_dict[ required_repo_info_dict_key ][ 1 ]
+                                        is_present = False
+                                        for repo_info_dict in all_repo_info_dicts:
+                                            for k, v in repo_info_dict.items():
+                                                if required_repo_info_dict_key == k:
+                                                    if tool_id == v[1]:
+                                                        is_present = True
+                                                        break
+                                        if not is_present:
+                                            all_repo_info_dicts.append( required_repo_info_dict )
                         all_required_repo_info_dict[ 'all_repo_info_dicts' ] = all_repo_info_dicts
         return all_required_repo_info_dict