We have cloned histone cDNAs from total RNA isolated from testis and from gastrula-stage embryos of the sea urchin Psammechinus miliaris. The reverse transcription of histone mRNAs was specifically primed with an oligonucleotide that is complementary to the conserved palindromic sequence present at the 3' end of nonpolyadenylated histone mRNAs. Two sperm H2B, two late H2B, and three late H2A variant cDNA clones were isolated and characterized by DNA sequence analysis. These cDNA clones were used to study the accumulation of histone mRNA during sea urchin embryogenesis. The different late H2A and H2B mRNAs are present in as few as 200 copies in the egg and each accumulate to 3-5 X 10(5) molecules in the gastrula embryo. One of the late mRNAs, the H2A-3 mRNA, is also abundant in testis RNA and codes for the H2A variant present in sperm chromatin. The late H2A-3 protein is therefore a more prevalent H2A variant of the sea urchin. In contrast, the two sperm H2B mRNAs are found in testes but not ovaries and embryos of the sea urchin, suggesting that the sperm H2B genes are expressed only during spermatogenesis. In addition, evidence for gene conversion between two late H2A gene variants is presented.