Nuclei isolated from sea urchin embryos incubated in vitro in the presence of S-adenosyl-[methyl-3H]methionine, methylate their own basic proteins. The protein methylase activity varies during the embryonic development with two peaks of activity at mesenchymal blastula and at young gastrula. Histones H3 and H4 are the main substrates of the reaction. The extent of methylation of the two histones depends on the S-adenosylmethionine concentration. At low S-adenosylmethionine concentrations, the in vitro methyl-accepting ability of H3 is 10-times that of H4, while at high concentrations it is 3-times that of H4. This finding is clearly evident in the equilibrium saturation experiments with blastula and gastrula nuclei, which both show two distinct Km values for S-adenosylmethionine. The major and perhaps only product of methylation is epsilon-N-methyl-lysine. Enzyme activity is clearly correlated with specific embryonic stages, while no correlation is apparent between enzyme activity and the amount of DNA in the embryos.