The Yilgarn and Pilbara regions of Western Australia are considered biodiversity hotspots for subterranean invertebrates. While the relatively well studied (aquatic) stygofauna are typically constrained to geographically isolated habitats (‘subterranean islands’) and have likely originated from multiple independent epigean ancestors, the troglofauna found in cavernicolous calcretes and fractured rock remains largely unstudied. Here we focus on the pseudoscorpion genera Tyrannochthonius Chamberlin, 1929 and Lagynochthonius Beier, 1951, as common components of the troglofauna, to determine whether they also display highly restricted distributional patterns, and have independent origins. Bayesian and maximum likelihood analyses of sequence data from the mtDNA cytochrome c oxidase I (COI) and the small subunit 18S nuclear genes for subterranean and epigean species from both genera reveal divergent mtDNA lineages that are restricted to single aquifers and/or geographic locations. This strong geographic structuring of troglobitic pseudoscorpions is indicative of short-range endemism and supports the ‘subterranean island’ hypothesis. Further, independent sister relationships between subterranean and epigean taxa indicate multiple invasions into subterranean habitats, likely driven by post-Miocene aridification, consistent with that predicted for the stygofauna. The phylogeny also reveals that Tyrannochthonius + Lagynochthonius is monophyletic but that Lagynochthonius is polyphyletic and nested inside Tyrannochthonius. The results of this study point to common processes that have shaped the diversity and uniqueness of both stygofaunal and troglofaunal communities in Western Australia.