The aye-aye is listed as one of the world’s 25 most endangered primates, in large part due to frag-mentation of their habitat. To protect aye-ayes, itis important to reconnect and maintain gene flow between historically connected populations. To better prioritize habitat conservation and restoration, we must identify the mechanisms for geneflow between populations. Previous research has shown high levels of differentiation between three northern aye-aye populations. Also, ranging patterns differ between sexes in this species; female home ranges are smaller than males’ and do not overlap other females’, whereas male ranges are large and overlap with both males and females. The large travel distances observed in males may reflect differences in dispersal patterns between the sexes. We used blood (n=5) and faecal (n=3) samples from eight wild aye-aye from four populations in northern and eastern Madagascar. We identified146 and 224 informative SNPs in the paternally-inherited Y-chromosome and maternally-inherited mtGenome respectively, and genotyped individuals using these loci. We used the phylogenetic tree tool in Galaxy to calculate pairwise genetic distance between all sampled individuals. Mean pairwise genetic distance based on mitochondrial markers was 0.68 compared to 0.37 in Y-chromosomal markers. In particular, mitochondrial loci revealed high genetic distance between individuals from two eastern populations, whereas Y-chromosomal loci revealed low genetic distance between these populations. In congruence between marker types may reflect male-biased dispersal in aye-ayes. Low distance between paternally-inherited markers may indicate historic connectivity along the eastern rainforest corridor, which should be considered in conservation planning