Genetic structure of populations of the red sea urchin, Strongylocentrotus franciscanus. Population subdivision was evaluated in the red sea urchin, Strongylocentrotus franciscanus, using DNA sequence data from 134 adult individuals collected in 1995 and 1996. On average 22 individuals were sequenced from six geographic locations between Alaska and Baja California (N=134), nearly the full extent of the species range. DNA sequence data was obtained from direct sequencing of a 273 base pair region of the bindin gene, which encodes a sperm fertilization protein. Results indicate that bindin is sufficiently polymorphic to serve as a genetic marker. We identified 14 unique alleles present in the entire range sampled with a maximum of eight alleles at a specific site. Mean pairwise comparison of the 14 unique alleles indicates moderate sequence diversity (p-distance=1.06). Although there is conflicting evidence to suggest that Alaska populations may deviate from the Hardy-Weinberg expectations, analysis of bindin genotype frequencies indicate that it is not possible to reject the null hypothesis of random mating throughout the species range. The results of a chi-square test with pooling conform to Hardy-Weinberg expectations for all populations (P>0.05) except for the Alaska population (P=0.037). Inbreeding coefficients are consistent with this result and suggest that for the bindin locus, there is high gene flow. These results are compared with previously published results of genetic substructuring in sea urchins to examine relationships among population structure, dispersal potential and biogeography.