Gekko hokouensis is widely distributed in southern Kyushu and Ryukyu Archipelago as well as Taiwan and eastern continental China, whereas the distribution of G. yakuensis, its close relative, is confined to southern Kyushu, Yakushima, Tanegashima and Magejima. It is known that these two species hybridize and the offspring is viable. Furthermore, the hybrid swarms that consist of post F1 generations are reported from a few localities of southern Kyushu. In Yakushima, it is suggested that relatively high proportion of putative hybrids exist in some of the localities where both G. hokouensis and G. yakuensis are found. In this study, distributions of the two species and their hybrids in Yakushima were surveyed in a finer geographical scale. G. hokouensis, G. yakuensis and their hybrids were determined on the basis of morphological characteristics. Further, putative hybrids are confirmed by allozyme analysis. Then, sampling site of each specimen is mapped using GIS. Also their potential habitat analysis was attempted and their ecological differences and similarities are discussed. This study revealed that the two species seldom occur sympatrically, possibly due to their habitat differences. It is further suggested that they hybridize along with the habitat gradient.