<p>Pangolins are considered the most trafficked mammals in the world with all eight species listed on CITES Appendix I. Despite this pervasive threat to their survival, there remains a limited understanding of genetic diversity and connectivity among populations of Asian pangolin species, hampering effective conservation management. We analysed mitogenome sequences of the Sunda pangolin (<i>Manis javanica</i>) from across their Southeast Asia continental distribution, as well as Borneo. Phylogenetic reconstruction revealed six lineages, with clear separation north and south of the Kangar-Pattani biogeographic line in southern Thailand, revealing clear differentiation between Sundaland and Indochinese Sunda pangolin lineages. Further divergence across an east–west divide was observed in central and northern Thailand, extending northwards towards China. Our results provide new insights into the evolutionary relationships among Sunda pangolin populations in Southeast Asia, building on other recent research in this field and helping to establish the species’ baseline phylogeography. These inferences will aid conservation planning and support the genetic traceability of the illegal pangolin trade.</p>