About 50 species of cave-obligate Leptodirini (Leiodidae) beetles have been described so far in Romania, most of them populating caves in the Apuseni Mountains (north-western Romania) and the Southern Carpathians. In this contribution, we present the first molecular phylogeographic study of the two troglobiotic Pholeuon species from the Apuseni Mountains. The two species are Pholeuon (s.str.) leptodirum and Pholeuon (Parapholeuon) gracile, endemic to Bihorului Mountains and Pădurea Craiului Mountains, respectively. To examine the genetic divergence within and between the two species we sequenced 571 bp of the mitochondrial COI gene in a total of 145 specimens, 56 specimens of the first species (collected in five caves) and 89 of the second species (collected in eight caves) across their geographic ranges. We found very low genetic variation, four haplotypes in P. leptodirum and seven haplotypes in P. gracile, and a maximum of 0.7% and 0.9% intraspecific divergence, respectively. However, a significant genetic divergence of 6.55% was found between species. The results are consistent with previous definitions of the two species based on morphological characters, while caution should be taken in considering attributions to different subspecies. Our research contributes to the phylogeographic information of troglobitic beetles, providing a solid basis for future comparison with other terrestrial or aquatic cave adapted species.