Foraminifers form an important link between bacteria and macrobenthos in natural food webs and thereby play a major role in biogeochemical cycling. There have been few studies conducted to clarify these relationships, although the biomass of foraminifera, particularly the soft-shelled monothalamous taxa, is high in the deep seas. Molecular tools are now being used to study evolution and genetic diversity in widely separated oceanic environments. However, the relationship between genetic diversity and the ambient environment is not well understood. To test the idea that environmental conditions can affect genetic diversity, we conducted molecular phylogenetic analyses based on clone analysis of environmental DNA for benthic foraminifers and environmental measurements in sediments from various oceanic environments. Monothalamous foraminifers were found in dysoxic (<45 μM), low-oxygen (<120 μM), and well-oxygenated (>120 μM) environments. The number of phylotypes was higher in the oxic environments of central Sagami Bay, Japan, and the east equatorial Pacific Ocean, than in the lower-oxygen areas of Sagami Bay. Phylotypes closely related to the genus Ovammina and some other saccamminids, as well as the calcareous genus Stainforthia, were preferentially found in lower dissolved-oxygen (DO) environments, while phylotypes of other saccamminids, Hippocrepinella, and an unidentified foraminiferal species, occurred at higher DO concentrations. Our analysis suggests that novel monothalamous phylotypes exist in habitats ranging from the sulfide-enriched environments of chemosynthetic ecosystems to those with high concentrations of DO as at the abyssal depths and in well-mixed bioturbated sediments.