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Previous research on the causes of craniometric variation within and among human populations has invoked both genetic and environmental explanations. Recent studies of modern populations in the United States and Portugal, among other populations, suggest that changes in environmental conditions have resulted in significant changes in cranial morphology. While similar changes in cranial morphology have been observed in genetically diverse populations, these populations do not appear to be converging on a common form. This study seeks to understand the role that population history and environmental variation play in explaining craniometric variation in the modern Portuguese. Using three-dimensional craniometric data collected from an identified skeletal collection from Lisbon, Portugal, this research examines the relationship between cranial morphology and place of birth. Two hypotheses are tested with regard to craniometric variation. The first asks whether phenotypic variation is related to geographic distance in the sample and therefore accurately represents genetic relationships. The second explores whether the significant secular changes observed in the sample obscure the population history reconstructed using craniometric data. The results demonstrate a significant relationship between geography and cranial morphology in the modern Portuguese sample. The clinal distribution to the craniometric variation is similar to what has been reported in some studies of molecular DNA from the Portuguese. The results show that cranial morphology reflects both the geography and genetic history of the sample and, furthermore, that secular changes in the population neither obscure nor erase this pattern. This study illustrates that even when secular changes have a significant impact on cranial morphology, they do not impede researchers’ ability to reconstruct genetic relationships using craniometric data.