The population structure of the deep-sea sponge-associated shrimp Spongicola japonica was investigated, and the mechanism of pair formation analysed from field samples. The composition pattern of shrimp in host sponges was divided into three patterns by sex and number as follows: solitary, a solitary inhabitant; sexually paired, a pair with a male and a female; grouped, multiple individuals excluding those designated as sexually paired. Juveniles usually remained grouped or solitary in a host cavity until the size at which gonadal maturity starts. Before forming sexual pairs, shrimp appear to have a free-living period outside the host, when the ovarian stages of females correspond to early to late vitellogenesis. Re-invasion is just before the first spawning, when females are in the ovarian stage of late vitellogenesis.