Awareness of pressures on subterranean habitats and their associated groundwater-dependent ecosystems has increased recently. Subterranean fauna provide critical services and can act as bioindicators; however, a significant portion of this diversity is unknown. The family Bathynellidae are neglected taxa of tiny subterranean crustaceans, with only 112 species described in 36 genera and three subfamilies worldwide. Their conservative morphology, small size, and delicate exoskeleton make their dissection, observation, and study very difficult. However, in recent years, molecular tools have been used to support morphology and reconstruct phylogenies to analyse the relationships among taxa and understand their origins. In this paper, using molecular and morphological data, we recognize 37–41 new Bathynellidae putative species from Australia, including a new genus and species (Queenslandbathynella gen. nov. spinosa sp. nov.), here described, belonging to a new subfamily (Queenslandbathynellinae subfam. nov.), expanding the morphological knowledge of the family. We present a multigene phylogeny inclusive of many described and undescribed taxa from Australia and worldwide, with four genes (cytochrome c oxidase subunit I and 16S, 28S, and 18S ribosomal RNA), that supports the erection of a new genus and subfamily, which provides a new molecular framework for Bathynellidae.