The morphological variations between different populations of modern Ryukyu wild boar found on Amami, Kakeroma, Tokunoshima, Okinawa, Ishigaki, and Iriomote islands are investigated in this study. The size of mandibles and length of M3 in males and females of age groups IV-V were compared. Then the bucco-lingual measurements of P3, P4, M1 and M2 were compared to the corresponding dimensions of a standard population using logarithmic ratio technique (LSI). Seven non-metrical characters of the mandible were compared between the populations. As a result, a different pattern was observed between mandibles and teeth. This was apparent especially in Ishigaki, where the size of mandibles of Sus was large compared to Amami, Okinawa, and Iriomote populations, but the size of teeth was small. The pattern of non-metrical characters was similar between Ishigaki, Iriomote, and Kyushu populations, with relatively high proportion of P1 and lost heptapreconulid ; Amami, Okinawa and Honshu populations comprised another group, with lost P1 and lost heptapreconulid. Based on the result of non-metrical analyses and size of teeth in the present study, the morphological characteristics of Sus from Tokunoshima and Okinawa were similar to Kakeroma and Amami and not to Ishigaki and Iriomote. Furthermore, the morphological characteristics of Sus from Tokunoshima and Kakeroma were more similar to Okinawa than to Amami in the base shape of the mandible and the relatively high proportion of the presence of a notch. The situation of Sus in Amami, with their size and shape differing the most from other modern Ryukyu wild boars, would appear to be the result of the island rule or the decline in body size exhibited by insular populations of artiodactyls compared with their mainland relatives. The Sus in Amami may have been separated for a longer period of time than other Ryukyu wild boars in the Nansei islands. The situation of Sus in Kakeroma and Tokunoshima was questionable since they had sizes and shapes more similar to Okinawa than to Amami despite their geographical locations. The study suggests a possibility of human interference in some of the islands where the wild boars live today. The present study has shown that by using the log ratio technique and non-metrical characteristics, it is possible to gain insight on the size and morphological variations of Ryukyu wild boars even for islands with only a small sample size.