Intraspecific allozymic variation and interspecific genetic divergence were studied in three sea urchin species of the genus Strongylocentrotus (S. intermedius, S. nudus, S. pallidus) from the Sea of Japan. S. pallidus and S. intermedius showed high mean values of expected heterozygosity, H(e)=0.223+/-0.072 (17loci) and H(e)=0.230+/-0.065 (19loci), respectively. This estimate was somewhat lower in S. nudus, H(e)=0.126+/-0.043 (17loci). Estimates of Nei's genetic distance between S. nudus/S. intermedius (D=1.578, 17loci) and S. nudus/S. pallidus (D=1.327, 15loci) were considerably higher than that between S. intermedius/S. pallidus (D=0.269, 17loci). Invoking the protein clock hypothesis and using Panamanian geminate sea urchins for protein clock calibration, the time of divergence between S. intermedius and S. pallidus was estimated as 2.7MY. The results obtained for S. intermedius and S. nudus by us differ considerably from results obtained for these species by Norimasa Matsuoka and coworkers. The revealed discrepancies are discussed and the conclusion made that Matsuoka and coworkers' data on echinoderm biochemical genetics and systematics should be used with caution.