Hybrid embryos were derived from reciprocal crosses of Strongylocentrotus purpuratus and Lytechinus pictus sea urchins. The expression of proteins specific for L. pictus was restricted in these hybrid embryos, while this was not so for most proteins specific for S. purpuratus. In particular, the aboral ectoderm-specific calcium-binding protein Spec1 was expressed at normal levels in hybrid embryos, but its L. pictus homologue, LpS1, was considerably reduced. LpS1 mRNA accumulated in hybrid plutei to only 4-5% of its normal level. Transcription of the LpS1 gene was substantially reduced in hybrid embryos, as determined by a nuclear RNA run-on assay. Southern blot analysis of genomic DNA indicated that there was no detectable loss or rearrangement of LpS1 DNA in hybrid embryos. Thus, the Spec1 gene is expressed normally in hybrid embryos, but the transcription of its homologue, the LpS1 gene, is considerably restricted.