Morphological, mitochondrial DNA, and single-copy nuclear DNA differences show that the tropical sea urchin Echinometra mathaei is composed of at least four independent gene pools. Evolutionary distance between species measured with restriction-site changes (for mitochondrial DNA) and thermal renaturation (for single-copy nuclear DNA) is 1%-3% nucleotide divergence. Thus these are the most closely related sea urchin species known. Despite this genetic similarity, strong blocks to interspecific fertilization exist in this genus. Between two Hawaiian species, few eggs are fertilized in hybrid crosses, even in the presence of excess sperm. Microscopic examination of such crosses shows that sperm attachment to heterologous eggs is inhibited. Measures of genetic distance between species can help reveal the tempo of speciation and allow comparisons of morphological, biochemical, and ecological characteristics to be made in an evolutionary framework. Our results show that strong reproductive isolation can evolve by changes in egg-sperm recognition without extensive genetic divergence between species. Such mechanisms are most easily studied in free-spawning animals such as sea urchins but as well may represent an important aspect of speciation in species with internal fertilization.