Vesicomyid clams are among the dominant invertebrates of chemosynthesis-based communities found at deep-sea cold seeps and hydrothermal vents, yet there is considerable taxonomic confusion within the family Vesicomyidae. The present study examined phylogenetic relationships among vesicomyid clams belonging to a cryptic-species complex that includes Vesicomya (previously Calyptogena) pacifica (Dall, 1891) and Vesicomya lepta (Dall, 1896). Mitochondrial (mt) COI sequences from clams collected between 1991 and 2001 along the western margin of North America from the San Clemente Basin (32°N latitude) to the Juan de Fuca Ridge (48°N latitude) revealed five discrete evolutionary lineages: V. pacifica (mt-type I), V. lepta (mt-type IV), and three undescribed species defined by mt-types II, III, and V. Separation of the three lineages defined by mt-types I, II, and III was also revealed by an independent nuclear gene (ribosomal ITS-1), and by DNA sequences from vertically transmitted bacterial endosymbionts found in the gills of these clams. Lineages I, II, and III occur in Monterey Bay, California, and the data suggest that bathymetric segregation may have played a role in their isolation and divergence.