The extent of historic forest cover across Madagascar is largely unknown and likely changed during Pleistocene glacial cycles. Additionally, current lemur species distributions do not reflect their historic ranges. Many lemur species are primarily arboreal and therefore distributions may have shifted along with forest habitat. Currently the central highlands consist primarily of grassland and are almost devoid of lemur species. The western-rainforest refugia model for Madagascar’s biodiversity suggests that at times of glacial minima, the eastern rainforest extended west, allowing dispersal of forest-dwelling species across the central high-lands. Recent research showed east-west geneflow in both brown and mouse lemur species. We tested for east-west gene flow within aye-ayes, one of the few lemur species that is distributed on both sides of the island. We sampled mitogenomes from seven populations across the aye-aye’s geographic distribution and calculated pairwise Fst among all populations. We used migrate-n to test models of gene flow across the central highlands between a population in the west and two populations in the east. We used Bayes factors to assess the relative support for these models. Population differentiation revealed the lowest Fst values between the West and Central-East populations (0.784), and greater differentiation between the more proximate West and North-West populations (Fst 0.959). The best supported model was asymmetric gene flow from east to west. Asymmetric gene flow and lower differentiation for populations either side of the central plateau suggest historic connectivity across the island for aye-ayes, thus offering further support for the western-rainforest refugia hypothesis.