diff --git a/src/main/scala/com/fulcrumgenomics/fastq/FastqToBam.scala b/src/main/scala/com/fulcrumgenomics/fastq/FastqToBam.scala
index 7a99ad20e..01e3f6998 100644
--- a/src/main/scala/com/fulcrumgenomics/fastq/FastqToBam.scala
+++ b/src/main/scala/com/fulcrumgenomics/fastq/FastqToBam.scala
@@ -97,6 +97,7 @@ class FastqToBam
   @arg(          doc="Read group ID to use in the file header.")                               val readGroupId: String = "A",
   @arg(          doc="The name of the sequenced sample.")                                      val sample: String,
   @arg(          doc="The name/ID of the sequenced library.")                                  val library: String,
+  @arg(flag='b', doc="Library or Sample barcode sequence.")                                    val barcode: Option[String] = None,
   @arg(          doc="Sequencing Platform.")                                                   val platform: String = "illumina",
   @arg(doc="Platform unit (e.g. '<flowcell-barcode>.<lane>.<sample-barcode>')")                val platformUnit: Option[String] = None,
   @arg(doc="Platform model to insert into the group header (ex. miseq, hiseq2500, hiseqX)")    val platformModel: Option[String] = None,
@@ -136,6 +137,7 @@ class FastqToBam
     val rg = new SAMReadGroupRecord(this.readGroupId)
     rg.setSample(sample)
     rg.setLibrary(library)
+    this.barcode.foreach(bc => rg.setBarcodes(util.Arrays.asList(bc)))
     rg.setPlatform(this.platform)
     this.platformUnit.foreach(pu => rg.setPlatformUnit(pu))
     this.sequencingCenter.foreach(cn => rg.setSequencingCenter(cn))
diff --git a/src/test/scala/com/fulcrumgenomics/fastq/FastqToBamTest.scala b/src/test/scala/com/fulcrumgenomics/fastq/FastqToBamTest.scala
index 888cf2560..7941e681c 100644
--- a/src/test/scala/com/fulcrumgenomics/fastq/FastqToBamTest.scala
+++ b/src/test/scala/com/fulcrumgenomics/fastq/FastqToBamTest.scala
@@ -270,6 +270,7 @@ class FastqToBamTest extends UnitSpec {
       output=bam,
       sample="foo",
       library="bar",
+      barcode=Some("TATA-GAGA"), //note that when passed a single string with a - separator like this, htsjdk prouduces two barcodes via getBarcodes()
       readGroupId="MyRG",
       platform="Illumina",
       platformUnit=Some("pee-eww"),
@@ -291,6 +292,9 @@ class FastqToBamTest extends UnitSpec {
     rg.getSample shouldBe "foo"
     rg.getLibrary shouldBe "bar"
     rg.getReadGroupId shouldBe "MyRG"
+    rg.getBarcodes() should have size 2
+    rg.getBarcodes().get(0) shouldBe "TATA"
+    rg.getBarcodes().get(1) shouldBe "GAGA"
     rg.getPlatform shouldBe "Illumina"
     rg.getPlatformUnit shouldBe "pee-eww"
     rg.getPlatformModel shouldBe "hiseq2500"