Described in 2005, Laonastes aenigmamus is the only species of Diatomyidae. The known distribution of this rodent encompasses only the rugged mountains of the Khammouan karst in central Lao People's Democratic Republic. We used a sample of 52 specimens to survey population structure by sequencing 887 base pairs of the cytochrome-b gene. The overall haplotype diversity was low (0.789 ± 0.039 SD), with 14 haplotypes identified, whereas the nucleotide diversity was high (0.015 ± 0.008 SD). Phylogenetic and haplotypic network reconstructions revealed 3 well-supported and rather divergent lineages with mutational steps ranging from 28 to 32. Identified haplotype groups correspond to localities, suggesting that populations of L. aenigmamus are geographically structured. Mismatch distributions suggest population stability. An exact test for population differentiation confirms a significant level of differentiation. Taking into account human pressure increasingly threatening this ecosystem, we provide preliminary insights on the genetically discrete population structure of this enigmatic mammal species.