Knowledge of the degree to which various subsets of morphological data reflect molecular relationships is crucial for studies attempting to estimate genetic relationships from patterns of morphological variation. This study assessed the phylogenetic utility of six different human cranial regions, plus the entire cranium. Three-dimensional landmark data were collected for 83 landmarks from samples of skulls from 14 modern human populations. The data were subsequently divided into anatomical regions: basicranium, upper face, mandible, temporal bone, upper jaw, cranial vault, and a subset of points from around the entire cranium. Depictions of population molecular distances were calculated using published data on microsatellites for the same or closely related populations. Distances based on morphological variation of each of the anatomical regions were compared with molecular distances, and the correlations assessed. The morphology of the basicranium, temporal bone, upper face, and entire cranium demonstrated the highest correlations with molecular distances. The morphology of the mandible, upper jaw, and cranial vault, as measured here, were not significantly correlated with molecular distances. As the three-dimensional morphology of the temporal bone, upper face, basicranium, and entire cranium appear to consistently reflect genetic relationships in humans, especially with more reliability than the cranial vault, it would be preferable to focus on these regions when attempting to determine the genetic relationships of human specimens with no molecular data. Am. J.Hum. Biol., 2009. © 2008 Wiley-Liss, Inc.