We describe the first complete sea urchin member of the H6 subfamily of homeobox genes. A cDNA encoding the complete protein was recovered from a Strongylocentrotus purpuratus library, and sequence comparisons demonstrate that this gene belongs to the same family as the Nkx-5.1, Nkx-5.2, and H6 genes of mammals, and the GH6 and SOHo-1 genes of chicken. In accord with current nomenclature this gene is named SpHmx. The gene is present in a single copy per haploid genome. Single-strand probe excess hybridization demonstrates that a rare maternal SpHmx mRNA is present in unfertilized eggs. Strong zygotic expression begins during the blastula stage, and the transcript is present at moderately high levels until late in development. Whole mount in situ hybridization reveals a remarkable pattern of expression: In midgastrula-stage embryos SpHmx is expressed throughout the archenteron, but particularly strongly in delaminating secondary mesenchyme cells. This more general expression resolves to a dramatic pigment cell-specific pattern in prism and pluteus stages. SpHmx apparently encodes a cell-type-specific transcription factor of embryonic pigment cells.