Abstract The community structure of the bathyal meiofauna of a cold-seep community found off Hatsushima in Sagami Bay, central Japan, was compared with the community composition outside the influence of the seep, using sediments collected during dives 226 and 227 of the deep-sea submersibleShinkai 2000. The sediment from the Hatsushima seep site (HSS) was very coarse, black in color, and with an odor of hydrogen sulfide, suggesting reduced thiobiotic conditions. The sediment from the control area was well-oxygenated, fine silt. Despite the differences in the characteristics of the sediments, the abundance of meiofauna in the HSS was not very different from that in the control area. However, its composition even at the major taxonomic group level was distinct; for example, a high nematode/copepod ratio occurred in one of the samples collected at the HSS. At the species level, nematodes were less diverse at the HSS than at the control area. The composition of the nematode fauna at the HSS showed stronger affinity with that collected at the adjacent control area than with a community sampled from other deep-sea environments or another seep community in shallow water. This emphasizes that the adaptation of nematodes to the thiobiotic condition is controlled by local conditions.