Patterns of genetic diversity in the groundwater fauna of Australia have largely focused on obligate stygobites of relatively large size, namely, crustaceans. Oligochaete worms, with their smaller size and broader ecological niches, provide a contrasting model in which to examine such patterns. Genetic diversity in subterranean oligochaetes in the Pilbara region of Western Australia were examined using one nuclear (18S) and two mitochondrial (COI, 12S) regions. The observed variation was assessed at three levels of hydrology – river basin, creek catchment, and individual bore or site – to document geographic patterns. Most species appeared to be restricted to an individual catchment; however, five species, representing three families, were widespread, with some haplotypes being shared between bores, catchments and even basins. General patterns suggest that while hydrology plays a role in the distribution of oligochaete species, it does not always confine them to catchments, in contrast to patterns observed in groundwater isopods and amphipods in the region. We suggest that intrinsic characteristics of oligochaetes, such as body size, shape, reproductive strategy and ecological requirements, may have allowed them greater dispersal within the subterranean biome of the Pilbara. In particular, oligochaetes may occupy subterranean and surface waters, increasing their opportunities for dispersal.