Skulls of the three species of Ryukyu spiny rats (Tokudaia osimensis, T. tokunoshimensis and T. muenninki) were osteometrically compared. In all measurements the size tendencies in which T. tokunoshimensis was the largest, T. muenninki middle, and T. osimensis the smallest were confirmed. However, the lengths of the molar row were exceptionally the largest in T. muenninki, middle in T. tokunoshimensis and the smallest in T. osimensis. The raw measurement data obviously indicated significant differences in size among the three species. We demonstrated that the neurocranium was larger in T. osimensis than in T. muenninki from the results of the proportional analyses. The principal component analyses using the raw measurement data also pointed out that the skulls from the three species were obviously distinguished in the charts, although the plots were not completely separated by the principal component analysis using the proportional indices. The CT images showed that both maxilla and palatine bone were thinner near the greater palatine foramen area and pointed out that the characteristic palatine structure fixed the position of the greater palatine foramen in each species of Tokudaia.