This study presents the late Quaternary faunal change of small mammals on the southern part of Okinawajima (Ryukyu Archipelago) on the basis of subfossils in late Pleistocene and middle Holocene fissure-filling deposits. The present subfossils include the Okinawa spiny rat Tokudaia muenninki, Ryukyu long-furred rat Diplothrix legata, Watase's shrew Crocidura watasei, and an indeterminate species of bat. With the exception of C. watasei, these species no longer exist in southern Okinawajima. Predominance of these rat species suggests that the environment around the fissure was densely forested during these ages. However, the presence of C. watasei remains implies that open habitats also existed in the middle Holocene. Tokudaia muenninki remains from the fissure show that it had survived on southern Okinawajima until the middle Holocene. The upper first molar widths and lower molar row lengths in the late Pleistocene T. muenninki material from the fissure are significantly smaller than those of extant conspecific specimens, whereas the upper molar row length appears to be similar to those of the extant conspecifics. These findings suggest that the molar proportions of T. muenninki have changed since the late Pleistocene.