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The Copper Age (3rd millennium BC) was characterized by considerable socioeconomic transformations and coincided with the discovery of metallurgy. In this study we reconstruct the peopling of Italy during this period on the basis of dental morphology traits. Dental remains from 41 sites throughout Italy were analyzed; only three of the sites (Laterza and two from Sicily) span from the late Copper Age to the early Bronze Age. To work with adequate samples, we pooled the collections into nine geographically and culturally homogeneous groups. Dental morphological traits were scored on 8,891 teeth from 1,302 individuals using the ASUDAS scale. The correlation between the mean measure of divergence and geographic distances (calculated as air distances) was computed. Multidimensional scaling with the minimum spanning tree and maximum-likelihood methods was applied to assess the relationships between groups. The results revealed a substantial genetic homogeneity among the populations throughout the Italian peninsula during the Copper Age with the exception of Sardinia, which tends to diverge from the continental samples. Phenetic and geographic distances correlate highly significantly only when the southern samples from Sicily and Laterza are removed from the analysis, which indicates that these groups may have experienced genetic admixture with external populations.