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Aim We compare the phylogeographical structure among caves for co‐occurring cave dwelling crickets (Ceuthophilus) in two subgenera Ceuthophilus (Ceuthophilus) (hereafter, called Ceuthophilus) and Ceuthophilus (Geotettix) (hereafter, called Geotettix). In our study area (central Texas), cave‐inhabiting members of the subgenus Ceuthophilus are trogloxenes, roosting in the caves but foraging above ground and occasionally moving between caves, whereas members of the subgenus Geotettix are near‐obligate cave dwellers, which forage inside the caves, and only rarely are found above ground. Differences in potential dispersal ability and ecology provide a framework for understanding their effects on the phylogeographical structure and isolation of populations of cave dwelling organisms. Location Edwards Plateau, Texas, USA. Methods We sequenced 1263 bp of two mitochondrial genes for a total of 309 individual rhaphidophorid cave crickets primarily in two subgenera of Ceuthophilus (Rhaphidophoridae). We reconstructed phylogenetic trees for each subgenus using Bayesian inference and then assessed whether their recent evolutionary history exhibited patterns of geographical structure. Results Both Ceuthophilus and Geotettix exhibited strong geographical structure. Rather than exhibiting the expected lower levels of divergence and genetic structure, the trogloxenes of the subgenus Ceuthophilus show deeper divergences than the more cave‐limited Geotettix taxa. Ceuthophilus has a higher proportion of unique haplotypes than does Geotettix. Mismatch distributions of Ceuthophilus and Geotettix differ, with Ceuthophilus exhibiting a multimodal mismatch distribution and Geotettix exhibiting a unimodal mismatch distribution. Main conclusions Both cave cricket subgenera display strong geographical structuring. However, their phylogenetic trees differed in their geographical orientation, which could be explained by timing of colonization, association with caves and underground connections, and above‐ground landscape or ecological barriers. For Ceuthophilus, the relatively high proportion of unique haplotypes and the multimodal mismatch distribution are consistent with relatively larger population size as compared to Geotettix.