SpHDAC1, a cDNA homolog of the yeast Rpd3 and higher eukaryotic histone deacetylases (HDAC), was cloned from the sea urchin Strongylocentrotus purpuratus. Its predicted polypeptide and the Rpd3 homologs were highly identical in two-thirds of their lengths, but diverged in their carboxyl-terminal regions in both length and sequence. SpHDAC1 transcripts, which reached maximal concentration at the blastula stages, and diminished thereafter, were neither ubiquitously expressed nor restricted to particular cell lineages, but appeared successively in distinct embryonic regions. In the blastula, transcripts were concentrated in a ring within the vegetal plate, comprising primordial endoderm, and, at the outset of gastrulation, in primordial hindgut endoderm. However, in early to mid-gastrula transcripts, they also appeared in oral ectoderm. In the late-stage gastrula, expression developed in the foregut. These shifts in spatial expression, together with an observed developmental blockage prior to sea urchin gastrulation by the histone deacetylase inhibitor trichostatin A, suggest a stepwise involvement of SpHDAC1 gene expression or SpHDAC1 functionality in the events of normal gastrulation.