diff --git a/public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java b/public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java
index 10326ef2e..507d4b786 100644
--- a/public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java
+++ b/public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java
@@ -245,7 +245,7 @@ public class FastaSequenceIndexBuilder {
      * Reset iterators and add contig to sequence index
      */
     private void finishReadingContig(FastaSequenceIndex sequenceIndex) {
-        sequenceIndex.add(new FastaSequenceIndexEntry(contig, location, size, (int) basesPerLine, (int) bytesPerLine, thisSequenceIndex++));
+        sequenceIndex.add(new FastaSequenceIndexEntry(trimContigName(contig), location, size, (int) basesPerLine, (int) bytesPerLine, thisSequenceIndex++));
         status = Status.NONE;
         contig = "";
         size = 0;
@@ -258,6 +258,14 @@ public class FastaSequenceIndexBuilder {
         }
     }
 
+    /*
+     * Trims the contig name to the expected value by removing any characters after the first whitespace
+     */
+    private static String trimContigName(final String contigName) {
+        int whitespaceIndex = contigName.indexOf(' ');
+        return ( whitespaceIndex == -1 ) ? contigName : contigName.substring(0, whitespaceIndex);
+    }
+
     /**
      * Stores FastaSequenceIndex as a .fasta.fai file on local machine
      * Although method is public it cannot be called on any old FastaSequenceIndex - must be created by a FastaSequenceIndexBuilder