diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py
index 822be16a268..637d0b6b581 100644
--- a/lib/galaxy/tools/parameters/dynamic_options.py
+++ b/lib/galaxy/tools/parameters/dynamic_options.py
@@ -127,9 +127,26 @@ class DataMetaFilter( Filter ):
             return file_value == dataset_value
         assert self.ref_name in other_values or ( trans is not None and trans.workflow_building_mode), "Required dependency '%s' not found in incoming values" % self.ref_name
         ref = other_values.get( self.ref_name, None )
-        if not isinstance( ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not isinstance( ref, galaxy.tools.wrappers.DatasetFilenameWrapper ):
+        is_data = isinstance( ref, galaxy.tools.wrappers.DatasetFilenameWrapper )
+        is_data_list = isinstance( ref, galaxy.tools.wrappers.DatasetListWrapper ) or isinstance( ref, list )
+        is_data_or_data_list = is_data or is_data_list
+        if not isinstance( ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not is_data_or_data_list:
             return []  # not a valid dataset
-        meta_value = ref.metadata.get( self.key, None )
+
+        if is_data_list:
+            meta_value = None
+            for single_ref in ref:
+                this_meta_value = single_ref.metadata.get( self.key, None )
+                if this_meta_value == meta_value:
+                    continue
+                elif meta_value is None:
+                    meta_value = this_meta_value
+                else:
+                    # Different values with mismatching metadata, return []
+                    return []
+        else:
+            meta_value = ref.metadata.get( self.key, None )
+
         if meta_value is None:  # assert meta_value is not None, "Required metadata value '%s' not found in referenced dataset" % self.key
             return [ ( disp_name, basic.UnvalidatedValue( optval ), selected ) for disp_name, optval, selected in options ]
 
diff --git a/test/functional/tools/dbkey_filter_multi_input.xml b/test/functional/tools/dbkey_filter_multi_input.xml
new file mode 100644
index 00000000000..7ecaeaaf943
--- /dev/null
+++ b/test/functional/tools/dbkey_filter_multi_input.xml
@@ -0,0 +1,34 @@
+<tool id="dbkey_filter_multi_input" name="dbkey_filter_multi_input" version="0.1.0">
+    <description>Filter select on dbkey of multiple inputs</description>
+    <command><![CDATA[
+        #for $input in $inputs#
+        cat $input >> $output;
+        #end for#
+    ]]>
+    </command>
+    <inputs>
+        <param format="txt" name="inputs" type="data" label="Inputs" multiple="true" help="" />
+        <param name="index" type="select" label="Using reference genome">
+          <options from_data_table="test_fasta_indexes">
+            <filter type="data_meta" ref="inputs" key="dbkey" column="1" />
+            <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
+          </options>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="output" />
+    </outputs>
+
+    <tests>
+        <!-- can choose a dbkey if it matches input -->
+        <test>
+            <param name="inputs" value="simple_line.txt,simple_line.txt" dbkey="hg19" />
+            <param name="index" value="hg19" />
+            <output name="output" file="simple_line_x2.txt"/>
+        </test>
+    </tests>
+
+    <help>
+    </help>
+</tool>
\ No newline at end of file
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 6fe5da9ac9b..e22459bbeed 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -17,6 +17,7 @@
   <tool file="multi_output_configured.xml" />
   <tool file="multi_output_assign_primary.xml" />
   <tool file="dbkey_filter_input.xml" />
+  <tool file="dbkey_filter_multi_input.xml" />
   <tool file="composite_output.xml" />
   <tool file="metadata.xml" />
   <tool file="metadata_bam.xml" />