Macaques are the most widely dispersed nonhuman primate, spanning across most of continental Asia and the Indonesian islands. Because males transfer out of their natal groups, male specific Y-DNA is relatively homogeneous across a species range. Females, however, do not leave their natal groups; thus, maternally inherited mtDNA shows clustered, heterogeneous patterns. Extreme female philopatry makes studying macaque Y-DNA and mtDNA very promising as mtDNA provides a robust molecular record of species bifurcations, whereas Y-DNA reveals more recent episodes of inter- and intraspecific genetic exchange. Previous data have uncovered – in violation of Haldane’s Rule – a geographically extensive introgression of rhesus macaque Y-DNA into Indochinese populations of the long-tailed macaque. Divergences in mtDNA sequence among the same species have pointed to possible common ancestors within the broader species complex. To clarify the evolutionary history of macaques in this ‘fascicularis species-group’, we are expanding earlier mtDNA and Y-DNA datasets, and subjecting the resultant sequences to phylogenetic analyses. The distinct evolutionary dynamics of these two genetic systems suggest they will record – in their topologies and divergence times – different details of the macaque radiation. The expectation is that mtDNA patterns will capture, for example, the colonization date of islands on the Sunda Shelf (Southeast Asia), whereas the Y-DNA will record the most recent period of genetic contact during a subsequent glacial peak. These data, coupled with knowledge of ancient sea-level changes in Southeast Asia, offer insight into the biogeography of macaques and a comparative model for hominin evolution.