We examined whether the shapes of the teeth could be used to distinguish morphological differences of modern Sus scrofa between subspecies, and between regions. The occlusal outlines of the lower teeth of five populations of the Ryukyu wild boar (S. s. riukiuanus) and two populations of the Japanese wild boar (S. s. leucomystax) were photographed and digitized into landmarks. The landmark coordinates were statistically compared among the populations. As a result, correct assignment rates of the populations based on their tooth shape was the highest for the fourth deciduous premolar. Pairwise test detected significant differences in tooth outline shape between the two subspecies. In addition, the tooth outline shapes of geographically adjacent populations tended to be similar. The results in this study indicated that the evaluation of tooth outline shapes, especially that of the fourth deciduous premolar, is a powerful approach for distinguishing subspecies of S. scrofa as well as for evaluating geographic variation among them. This method is useful in archaeological and paleontological studies because of its applicability for isolated teeth, and has potential to increase our understanding about the history of macroevolution, migration, and introduction of S. scrofa in the Japanese archipelago.