Phylogeographic reconstructions of co-distributed taxa can help reveal the interplay between abiotic factors, such as altitude and climate, and species-specific attributes, in shaping patterns of population genetic structure. Recent studies also demonstrate the value of both range-wide sampling and species distribution modeling (SDM) in comparative phylogeography. Here we combine these approaches to study the population histories of four phylogenetically-related forest-dependent bat species. All are endemic to the mountainous island of Taiwan but show differences in their tolerance to altitude, with Murina gracilis considered to be a high altitude specialist, M. recondita and Kerivoula sp. low altitude specialists, and M. puta an altitudinal generalist. We tested the prediction that contrasting habitat preferences would impact on patterns of past and contemporary gene flow, and found broad concordance between the results of population genetic analyses and MIROC-based species distribution models. Both lowland species showed evidence of genetic divergence between the east and west of the island, consistent with SDMs that indicated the Central Mountain Range (CMR) has presented a long-term and continuous barrier to gene flow since before the Last Glacial Maximum. In contrast, Murina gracilis and M. puta showed lower degrees of historical isolation and genetic differentiation associated with the CMR, reflecting greater gene flow, possibly coupled with past population growth in M. puta. Together our results highlight the usefulness of combining distribution models with phylogeographic analyses to understand the drivers of genetic structure.