In most humans, levels of lactase, an enzyme encoded by LCT, decrease after weaning. This leads to a reduced ability to digest lactose, referred to as “lactase non-persistence” (LNP). However, some individuals maintain high expression of lactase and are able to digest lactose into adulthood, referred to as “lactase persistence” (LP). LP is a recent adaptive trait in humans and has evolved in populations that practice milk production and consumption. We sequenced 594 bp in intron 13 of MCM6, a candidate enhancer region for LCT where LP-associated variants have been identified in European and African populations. Our sample consists of 641 individuals from 4 Tanzanian populations and 650 individuals from 19 Ethiopian populations that practice diverse subsistence methods. In addition to genetic data, we used phenotypic data from a lactose tolerance test to conduct a genotype-phenotype association analysis in 209 Tanzanians and 150 Ethiopians. The association between LP and the C-14010 variant in Tanzania was confirmed. For the first time we identified the presence of the C-14010 and G-13915 variants in the Hadza of Tanzania, who are traditionally hunter-gatherers. The G-13915 variant had not been identified in Tanzanian populations previously studied. The G-13907 variant was not found in the Tanzanian populations, though we identified it in the Ethiopians, consistent with work done by previous researchers indicating that this variant originated in Northeast Africa. Network analyses and tests of natural selection were performed to reconstruct the evolutionary history of this locus and to trace historic migration events in East Africa.