<p>We studied the genetic connectivity of wrinkle-lipped free-tailed bat (<i>Mops plicatus</i>, formerly <i>Chaerephon plicatus</i>) in Thailand, where this highly mobile species is known to inhabit 18 caves. Populations of <i>M. plicatus</i> are experiencing a drastic decline. Understanding genetic connectivity is crucial for assessing vulnerability to reduced gene flow and inbreeding. Using non-invasive genetic sampling, we analyzed mitochondrial (cyt<i>b</i> and D-loop) and nuclear DNA (SNPs) from 501 individuals across nine cave colonies over a 500&#xa0;km range. Our analysis revealed moderately high haplotype diversity in cyt<i>b</i>, high diversity in D-loop sequences, and low nucleotide diversity in both mitochondrial markers. F_<i>ST</i> analyses of nuclear and mitochondrial DNA showed consistently low values, indicating little to no differentiation. Additionally, F_<i>IS</i> values for nuclear DNA were likewise low, and Bayesian clustering indicated the absence of genetic structuring, suggesting a single, connected population. These findings suggest that the <i>M. plicatus</i> population in Thailand maintains genetic connectivity among cave populations through high gene flow, with no signs of inbreeding. Mismatch distribution analyses of mtDNA across all studied bat individuals suggest a sudden population expansion during the Early Pleistocene, whereas stairway plots of nDNA indicate a long-term stable population with two distinct growth events, one having occurred during the Middle Pleistocene and another in the Late Holocene, respectively. In conclusion, our findings recommend managing and conserving the wrinkle-lipped free-tailed bats in Thailand as a single population, with consistent conservation measures across all colonies.</p>