A new species of Ryukyu spiny rat, Tokudaia tokunoshimensis was described in the specimens originating from Tokunoshima Island in the southernmost region of Japan. The populations of Tokudaia are separately distributed only in Amami-Oshima, Tokunoshima, and Okinawa-jima Islands. We have described the osteological and external morphological characteristics and clarified the osteometrical distinctions among the three populations using the skull and skin collections. All external dimensions of head and body length, tail length, hindfoot length and ear length were larger in the Tokunoshima population than in the other two in mean value. The raw osteometrical data separated the Tokunoshima Island population from the other two in all measurements except for the length of molar row in the Okinawa-jima Island population. The principal component analysis also demonstrated that the skulls from the Tokunoshima Island population were morphologically distinct from those of the other populations. Here, from these findings, we point out that the Tokunoshima population of Tokudaia should be regarded as an independent species from the two other populations.