Basal experiments that examine the impact of hypoxia on bivalves provide an explanation for dominant bivalve population maintenance in hypoxic soft-bottom habitats. We conducted laboratory experiments to assess the effect of persistent anoxia on the survival of three bivalve species: Manila clams (Ruditapes philippinarum), ark shells (Anadara kagoshimensis), and Veremolpa micra. Further, we compared the interspecific variation of ark shells among different habitats in the intertidal and subtidal regions of Ariake Bay and Lake Nakaumi, Japan. A marked inter- and intraspecific variation was detected with respect to survival under anoxic conditions. Specifically, the survival of V. micra and ark shells in Lake Nakaumi under persistent anoxia was significantly higher than that of ark shells in Ariake Bay and Manila clams in Tokyo Bay. Further experiments indicated that ark shell survival (LT₅₀) under persistent anoxia with sulfurization was significantly lower than that under anoxia alone. Such inter- and intraspecific variations in anoxia and sulfurization tolerance might reflect the dominance of certain bivalve species in hypoxic regions.