Yamaguchia toyensis n. sp., n. gen. is described from an oligotrophic caldera lake, Lake Toya, Hokkaido, Japan. Although the taxonomic affinities are unknown, the genus differs from all other Lumbriculidae in having the combination of testes and atria in X, a single, prosoporous male funnel per atrium, and spermathecae in XI. Unlike other Japanese lakes that have thus far been surveyed, Lake Toya supports abundant populations of lumbriculids in the profundal benthos.