Skull morphology of Mustela itatsi from two islands adjacent to Kyushu, Kamikoshikijima and Yakushima Isls., Kagoshima Prefecture were compared with populations from mainland Japan. Although size and shape variation of these island populations were within whole species range of variation, the size variation was less than that of some mainland populations. In contrast, canonical variate analysis showed a separation of the Yakushima population from other populations compared. Between these islands, skull shape was different, indicating that ecological difference such as prey size and abundance may exist. Island populations of M. itatsi could have been differentiated from mainland populations depending on different ecological conditions and geological history of each island.