This study investigates whether variants in dental morphology and nuclear DNA provide similar patterns of intergroup affinity among regional populations using biological distance (biodistance) estimates. Many biodistance studies of archaeological populations use skeletal variants in lieu of ancient DNA, based on the widely accepted assumption of a strong correlation between phenetic‐ and genetic‐based affinities. Within studies of dental morphology, this assumption has been well supported by research on a global scale but remains unconfirmed at a more geographically restricted scale. Paired genetic (42 microsatellite loci) and dental (nine crown morphology traits) data were collected from 295 individuals among four contemporary Kenyan populations, two of which are known ethnically as “Swahili” and two as “Taita;” all have well‐documented population histories. The results indicate that biodistances based on genetic data are correlated with those obtained from dental morphology. Specifically, both distance matrices indicate that the closest affinities are between population samples within each ethnic group. Both also identify greater divergence among samples from the different ethnic groups. However, for this particular study the genetic data may provide finer resolution at detecting overall among‐population relationships. Am J Phys Anthropol 157:295–304, 2015. © 2015 Wiley Periodicals, Inc.