Abstract <p>In line with the new coronavirus occurrence, bats are an importantcarrier of viruses, which are extremely important to public safety. <i>Hipposideros armiger</i> is a large batspecies with a wingspan of approximately 50–60 cm. A comparativelylarge body and wingspread lead to a greater dispersal ability, whichin turn leads to a wider habitat. In this study, we employed theCYTB gene sequence (1117 bp) derived from <i>H.armiger</i> within five caves of southern Anhui provinceto undertake the landscape genetics research across the mountainousregion. Our study revealed the relatively low genetic variation observedin all five populations. Two clades were distinguished within thephylogenetic tree of 7&#xa0;haplotypes, and significant population differentiation(<i>F</i> _ST)was detected among all populations by AMOVA. In terms of the geographicaldistance, the group from the Caihuadong cave (CHD) exhibits a relativelyclose distance to the group from the Longkoudong cave (LKD) butshows the largest genetic distance. Additionally, both show a relativelyindependent clustering pattern based on haplotypes, particularlyCHD (H1, H2). The bats from the Yanzidong cave (YZD) shares a commonhaplotype (H3) with all other populations and lowest genetic diversity,suggesting the formation of this population might have been influencedby the founder effect. The mantel test between geographical andgenetic distances indicates a relatively weak correlation among <i>H. armiger</i> populations at a smallscale, further suggesting their robust dispersal capabilities, whichalso is supported by the AMOVA results. In population demography,only CHD shows a significant population expansion, which correspondsto its geographic environment being suitable for the survival of <i>H. armiger</i>, consistent with networkanalysis. This study provides an initial analysis of the landscapegenetic structure of <i>H. armiger</i>,offering a foundational reference for larger scale population geneticsin this species.</p>