The population genetics of P. lucasi was inferred using 1,061 base pairs (bp) of the Cytochrome b mitochondrial gene. A total of 77 individuals were classified a priori according to their localities, namely, Miri, Kuching, Sri Aman and Kelantan. Results showed that the populations of P. lucasi were separated into two haplogroups, namely, Haplogroup 1 (found in Miri and Kuching populations) and Haplogroup 2 (Miri, Kuching, Sri Aman and Kelantan populations). This separation was supported by bootstrap values in the phylogenetics analyses (94.9% in the maximum likelihood and 100% in Bayesian). A high level of genetic divergence was detected between two haplogroups (3.88%) and this separation could be related to historical events which include multiple colonisation and Pleistocene refugia during the Last Glacial Maximum ice age period. High genetic divergence within Miri (4.93%) and Kuching (4.72%) populations could be due to the presence of a species complex within the P. lucasi populations. The presence of haplotypes from both the populations in Haplogroup 1 and Haplogroup 2 might be due to the ability of this particular species of bats to perform long-distance flight for foraging. A high gene flow between these populations suggests a widespread female gene flow of P. lucasi, judging from the distance of both localities. Meanwhile, the absence of a deep structure from the haplotype trees further proves that P. lucasi may have had a wide dispersal ability since the Pleistocene has allowed for genetic exchange to occur between the regions in Malaysia.