Dental phenotypic data are often used to reconstruct biological relatedness among past human groups. Teeth are an important data source because they are generally well preserved in the archaeological and fossil record, even when associated skeletal and DNA preservation is poor. Furthermore, tooth form is considered to be highly heritable and selectively neutral; thus, teeth are assumed to be an excellent proxy for neutral genetic data when none are available. However, to our knowledge, no study to date has systematically tested the assumption of genetic neutrality of dental morphological features on a global scale. Therefore, for the first time, this study quantifies the correlation of biological affinities between worldwide modern human populations, derived independently from dental phenotypes and neutral genetic markers. We show that population relationship measures based on dental morphology are significantly correlated with those based on neutral genetic data (on average r = 0.574, p < 0.001). This relatively strong correlation validates tooth form as a proxy for neutral genomic markers. Nonetheless, we suggest caution in reconstructions of population affinities based on dental data alone because only part of the dental morphological variation among populations can be explained in terms of neutral genetic differences.