This paper provides new information on the distribution of Japanese native Vigna species in the subgenus Ceratotropis. The azuki bean complex (Vigna angularis) in Japan consists of cultigen, wild, weed and complex population types. Population genetic studies of this complex based on AFLP and RAPD analyses have revealed clinal variation in Japan. Population analyses have also provided support for hypotheses related to the origin of weedy azuki bean. The complex population type displays greater genetic variation than other population types in the azuki bean complex. Thus complex populations are the logical focus for both in situ and ex situ conservation. The wild and weedy Vigna species of Japan are a potential source of useful traits for agriculture and agriculturally related industries. Currently V. riukiuensis (V. minima subsp. minor var. minor) is being used as a bridging species to enable gene transfer among sexually incompatible Vigna cultigens. The potential of the genus Vigna to become a genetic model to enhance the understanding and genetic improvement of the tropical grain legume cultigen group is discussed.