The Garamantes flourished in southwestern Libya, in the core of the Sahara Desert ∼3,000 years ago and largely controlled trans-Saharan trade. Their biological affinities to other North African populations, including the Egyptian, Algerian, Tunisian and Sudanese, roughly contemporary to them, are examined by means of cranial nonmetric traits using the Mean Measure of Divergence and Mahalanobis D2 distance. The aim is to shed light on the extent to which the Sahara Desert inhibited extensive population movements and gene flow. Our results show that the Garamantes possess distant affinities to their neighbors. This relationship may be due to the Central Sahara forming a barrier among groups, despite the archaeological evidence for extended networks of contact. The role of the Sahara as a barrier is further corroborated by the significant correlation between the Mahalanobis D2 distance and geographic distance between the Garamantes and the other populations under study. In contrast, no clear pattern was observed when all North African populations were examined, indicating that there was no uniform gene flow in the region. Am J Phys Anthropol 147:280–292, 2012. © 2011 Wiley Periodicals, Inc.