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Matrix correlation represents an innovative methodology to evaluate the explanatory power of several hypotheses by measuring their correspondence with observed morphological variation. In this paper, we view the origins of Patagonians from a matrix correlation approach. Personal and published data on nonmetric cranial traits were used to estimate a biological distance matrix involving five major groups from Patagonia and two from the northwest and northeast regions of Argentina. To evaluate correspondence with other important factors, we used a geographic distance matrix and four design matrices, representing several patterns of settlement and differentiation. Biological distance was found to be strongly associated with spatial separation; the correlation between geography and nonmetric cranial distances was highly significant. When geographic distance is held constant, correlation between a model representing high levels of heterogeneity between the samples and morphological (nonmetric) variation becomes highly significant.