Objectives Cyclical submergence and re‐emergence of the Sunda Shelf throughout the Pleistocene served as a dynamic biogeographic landscape, across which long‐tailed macaques (Macaca fascicularis) have migrated and evolved. Here, we tested the integrity of the previously reported continental‐insular haplotype divide reported among Y and mitochondrial DNA lineages across multiple studies. Materials and Methods The continental‐insular haplotype divide was tested by heavily sampling wild macaques from two important biogeographic regions within Sundaland: (1) Singapore, the southernmost tip of continental Asia and (2) Bali, Indonesia, the southeastern edge of the Indonesian archipelago, immediately west of Wallace's line. Y DNA was haplotyped for samples from Bali, deep within the Indonesian archipelago. Mitochondrial D‐loop from both islands was analyzed against existing data using Maximum Likelihood and Bayesian approaches. Results We uncovered both “continental” and “insular” Y DNA haplotypes in Bali. Between Singapore and Bali we found 52 unique mitochondrial haplotypes, none of which had been previously described. Phylogenetic analyses confirmed a major haplogroup division within Singapore and identified five new Singapore subclades and two primary subclades in Bali. Discussion While we confirmed the continental‐insular divide among mtDNA haplotypes, maintenance of both Y DNA haplotypes on Bali, deep within the Indonesian archipelago calls into question the mechanism by which Y DNA diversity has been maintained. It also suggests the continental‐insular designation is less appropriate for Y DNA, leading us to propose geographically neutral Y haplotype designations.