Abstract Gene frequency distributions in subdivided populations are affected by migration of individuals between groups. This paper considers the effects of such migration on blood protein allele frequency distributions in social groups of the Cayo Santiago rhesus macaque colony. Gene frequencies for complete social groups and their migrant and natal segments were analyzed at four points within a four year period in the colony's history. Gene frequencies varied between the migrant segments of different groups. Gene frequencies of migrant segments of particular groups also varied substantially with time. Usually, but not always, the presence of migrants in groups reduced the levels of inter-group gene frequency differentiation. We suggest that our findings are explained by a model in which the recruitment of immigrants into social groups is largely random with respect to individual genotypes. Such a model implies that migration contributes to both stochastic and directed changes in gene frequencies in rhesus and similarly substructured populations.