Phylogeographic and feeding ecological studies of seven terrestrial mustelid species (Carnivora, Mustelidae), the Japanese marten Martes melampus, the sable Martes zibellina, the Japanese badger Meles anakuma, the ermine or the stoat Mustela erminea, the Japanese weasel Mustela itatsi, the least weasel Mustela nivalis, and the Siberian weasel Mustela sibirica, representing four biogeographic patterns in the Japanese archipelagos (Hokkaido, Honshu-Shikoku-Kyushu, Tsushima, and Hokkaido-Honshu), were reviewed in order to clarify causes for the faunal assemblage processes of those mustelid species in Japan. Here, three main constraints were extracted as important factors on the mustelid assemblage. First, fundamental evolutionary differences maintained by niche conservatism in each ecologically diversified lineage ("evolutionary constraint") would enable the species to co-occur without any major problem (coexistence among Martes, Meles, and Mustela species). Second, "ecological constraints" would force two closely related species to be allopatric by competitive exclusion (Mu. itatsi and Mu. sibirica) or to be sympatric by resource partitions (Mu. erminea and Mu. nivalis). Third and most importantly, "geological constraints" would allow specific species to be embraced by a particular geographic region, primarily deciding which species co-occurs. The allopatric distribution of two Martes species in Japan would have been established by the strong effect of the geological separation in Tsugaru Strait. Elucidating both phylogeny and ecology of co-existing species in a community assemblage is important to know which species possess distinct lineage and which ecological traits are adapted to local environments, fulfilling the requirement of the field of conservation biology that endemism and adaptation should both be considered. The Japanese archipelagos would, therefore, provide valuable insight into the conservation for small carnivoran species.