The distribution of Virgulinella fragilis and the hydro-environment of Aso-kai Lagoon, central Japan, were studied to clarify the foraminifer’s adaptation to low-oxygen conditions. The hypolimnion of the lagoon is oxygen-poor during much of the year. Two faunas (A and B) are recognized, based on cluster analysis. Cluster A fauna consists of species common in brackish lagoons, such as the genera Trochammina and Ammonia, and occurs in seasonally oxygenated waters. Virgulinella fragilis, the predominant species of Cluster B fauna, dominates the central part of the lagoon. This species can tolerate more severe oxygen deficiencies than the typical brackish foraminifers (e.g. Trochammina spp.) and can adapt to long periods of oxygen-poor conditions in coastal lagoon environments, as well as in pelagic to hemi-pelagic settings. In order to survive in the near-anoxia of Aso-kai Lagoon, V. fragilis may have adapted to environments in which little reactive iron is available in the sediment, leaving pore-water and bottom-water sulphide available for symbionts, or may utilize sulphur denitrification processes.