The karst habitats of central Texas, USA, support a diverse assemblage of endemic subterranean-obligate (troglobiotic) invertebrates, including several species of rove beetles (Coleoptera: Staphylinidae: Pselaphinae). This study generated a molecular dataset using sequence capture of Ultra-Conserved Elements (UCEs) to investigate species relationships and diversification patterns within this group. The analysis focused on species of the genera Batrisodes and Texamaurops, with particular attention to the federally endangered species Batrisodes texanus and Batrisodes cryptotexanus. Within the Travis and Williamson County cave-dwelling lineages, four well-supported clades were identified that broadly correspond to previously recognized geologic barriers to dispersal defined as karst fauna regions (KFRs). The results indicate a northward pattern of diversification among these lineages. The clades correspond to: (A) Texamaurops reddelli in the Jollyville Plateau KFR; (B) Batrisodes reyesi in the West Cedar Park and Post Oak Ridge KFRs; (C) Batrisodes reyesi in the McNeil–Round Rock KFR; and (D) a combined lineage of Batrisodes cryptotexanus and Batrisodes texanus in the Georgetown and North Williamson KFRs. However, the morphologically defined species Batrisodes texanus and Batrisodes cryptotexanus were not recovered as reciprocally monophyletic in phylogenetic analyses and did not form two distinct groups in clustering analyses of single-nucleotide polymorphisms (SNPs). Instead, the results supported the presence of five major subclades and five to seven genetic clusters. These patterns suggest that diversification and subsequent isolation of lineages likely occurred as karst habitats became progressively available over time within the North Williamson and Georgetown KFRs, influenced by geological processes such as faulting, structural changes, and drainage basin evolution. Comparisons with cave habitat resiliency assessments indicated that four genetic clusters occur within habitats that retain at least partial resilience, whereas three clusters are restricted to caves with low or impaired resiliency. Overall, integrating the genetic findings of this study with results from other molecular studies of co-occurring troglobiotic invertebrates highlights the importance of considering additional geological substructure within the North Williamson KFR when developing conservation strategies for these rare subterranean lineages and their habitats.