The formation of the Australian arid zone, Australia's largest and youngest major biome, has been recognized as a major driver of rapid evolutionary radiations in terrestrial plants and animals. Here, we investigate the phylogenetic diversity and evolutionary history of subterranean short-tailed whip scorpions (Schizomida: Hubbardiidae), which are a significant faunal component of Western Australian hypogean ecosystems. We sequenced two mitochondrial (12S, COI) and three nuclear DNA markers (18S, 28S, ITS2) from ∼600 specimens, largely from the genera Draculoides and Paradraculoides, including 20 previously named species and an additional 56 newly identified operational taxonomic units (OTUs). Phylogenetic analyses revealed a large and rapid species radiation congruent with Cenozoic aridification of the continent, in addition to the identification of a new genus in Western Australia and the first epigean schizomid from the Pilbara. Here, we also synonymise Paradraculoides with Draculoides (new synonymy), due to paraphyly and a lack of reliable characters to define the two genera. Our results are consistent with multiple colonisations of the subterranean realm from epigean ancestors as their forest habitat fragmented and retracted, with ongoing fragmentation and diversification of lineages underground. These findings illustrate the remarkable diversity and high incidence of short-range endemism of Western Australia's subterranean fauna, which has important implications for identifying and managing short-range endemic subterranean fauna. They also highlight the advantages of including molecular data in subterranean fauna surveys as all specimens can be utilized, regardless of sex and life stage. Additionally, we have provided the first multi-gene phylogenetic framework for Australian schizomids, which will enable researchers and environmental consultants to identify new taxa or align them to existing lineages.