The Pilbara bioregion (Western Australia) has become a hotspot for subterranean fauna as a consequence of many surveys conducted to comply with Western Australian environmental regulation requirements. In this bioregion, mining developments can have major implications for subterranean fauna and their conservation. However the diversity and species distributions of most taxa are still poorly known, including the crustacean family Parabathynellidae. Recent studies on a widespread genus of this family (Atopobathynella) from the Pilbara highlighted several undescribed taxa with interesting patterns of distribution. In the Gudai Darri locality, the northern flank of the Hamersley Range occurs as a stepped escarpment intersected by dykes and gullies, with groundwater occurring within fractured rocks abutting the Fortescue River valley, where a separate regional aquifer occurs. This investigation aimed to observe whether stygofauna species distributions (1) reflected the separation between the two major aquifers within the Hamersley Range and the Fortescue Valley; and (2) were influenced by the presence of dykes. We examined the Atopobathynella species occurring in the study area using morphological and molecular data. The results reflected the hydrogeological complexity of the study area with six new lineages of Atopobathynella, recorded mainly in different gullies, that do not share a most recent common ancestor. Two species are described here A. pagetae sp. nov. and A. lythei sp. nov., and four additional species are delineated through preliminary morphological analyses and molecular data. This study will improve future environmental impact assessments and the understanding of Parabathynellidae taxa distribution in hydrogeological complex areas.