Biochemical genetic variation at 12 allozyme loci was examined among three sympatrically occurring clam species (Astarte borealis, A. elliptica and A. striata: Bivalvia, Mollusca) from a single location off the east coast of Newfoundland, Canada. Nei's (1978) genetic distance (D) values for pairwise comparisons between the species ranged from 0.445 (between A. borealis and A. elliptica) to 0.530 (between A. borealis and A. striata) indicating speciation events ≈2.2–2.7 Myr BP. The timing of these speciation events is consistent with the proposed period of rapid speciation among the North Atlantic bivalve fauna following a significant extinction event (or events) ≈3.0 Myr BP. Allozyme variation among the three species was limited to allele frequency differences, with no absolute (fixed) differences being observed. The absence of diagnostic allelic differences in light of the large Nei's D-values is most unusual. The most plausible explanation is a form of balancing selection, whereby selection for the retention of ancestral alleles has prevented genetic diversity from increasing among the species via drift. Thirty of 36 exact tests for genetic differentiation were highly significant, indicating that the three species are genetically differentiated at these loci despite the absence of fixed allelic differences among the species. Compared with Hardy–Weinberg expectations, the allozyme loci exhibited heterozygote deficiencies which were highly statistically significant in all but one case. Two phenomena appear to account for the unusually large FIS values observed for all three species: first, inbreeding resulting in part from the extremely limited dispersal capabilities of the species, and second, a microgeographical Wahlund effect possibly operating at a scale of only tens of metres. Despite the absence of fixed allozyme differences, multivariate analyses of 14 morphometric traits and of allozyme variation at 12 loci both provided evidence of a high degree of genetic differentiation among the three species. Given the ability of the multivariate analyses of the allozyme and morphological variation to distinguish among sympatric A. borealis, A. elliptica and A. striata, it is suggested that the application of such analytical techniques on a larger scale will provide answers to long-standing questions about the uncertain taxonomy and systematics of the genus Astarte.