The aim of this study was to assess morphological differences between early-modern (Edo) Japanese and contemporary Japanese using recently uncovered human female remains at the Ikenohata-Shichikencho site in the Tokyo urban area. In this study, 30 female skeletal remains that still retained the upper and lower first molars and central incisors were selected [early-modern (Edo) Japanese group]. Forty contemporary female Japanese were selected as a control. Analyses by standard methods of geometric morphometrics revealed some morphological differences between the early-modern (Edo) Japanese group and the contemporary Japanese group. For example, the early-modern (Edo) Japanese group exhibited bimaxillary dentoalveolar protrusion, a flat occlusal plane, and a large S-N length. On the other hand, the contemporary Japanese group exhibited slight protrusion of the anterior nasal spine. These findings may be of interest to orthodontists who are studying age variation or temporal differences and could lead to a better understanding of morphological diversity and variability.