This study investigated interpopulation genetic relationships in the Jomon Atsumi Peninsula area, comparing the pattern of human migration revealed by strontium isotope ratio with dental metric variation of Yoshigo and Inariyama skeletal remains. Morphological differences were evaluated between the local and immigrant groups to determine whether or not local populations had become completely homogenized by human migration. We have constructed 4 × 4 contingency tables consisting of four clusters derived from K-means clustering of dental measurements and four groups (immigrants and locals of the two sites), and evaluated their correlations by Fisher’s exact test. The results revealed that human migration pattern was significantly correlated with dental metric variation, suggesting that there was regional heterogeneity among Jomon populations in the Atsumi Peninsula area. Although the distinction between immigrants and locals of Yoshigo and Inariyama populations based on strontium isotope analysis was not completely in accord with dental metric variability, most of the identified immigrants exhibited dental profiles that were beyond each local profile as determined using principal component analysis. Furthermore, the dental metric variances of the immigrants were significantly larger than those of the locals, suggesting multiple origins. The microdifferentiation among populations in the Atsumi Peninsula area may suggest nonrandom kin-structured migration and/or population aggregation from surrounding areas.