A species flock of the freshwater isopod genus Eophreatoicus Nicholls lives in seeps, springs and perched aquifers at the base of the Arnhem Plateau and associated sandstone outliers in Australia’s Northern Territory. These species have been found to have surprisingly high levels of genetic divergence and narrow range endemism, despite potential opportunities for dispersion during the summer monsoon season when streams flow continuously and have connectivity. Species of Eophreatoicus were identified morphologically as distinct taxa, sometimes with two or three species occurring at the same site. DNA sequence data from the mitochondrial 16S rRNA and cytochrome c oxidase subunit I genes corroborate our morphological concepts to a high level of resolution, with the exception of two distinct species that are identical genetically. The value of mtDNA data for identification of these species, therefore, is limited. These isopods disperse downstream from their home springs to a limited extent during the wet season, but the genetic data show that migration to non-natal springs, and reproduction there, may be rare. We argue that the multiplication of the narrow-range endemic species is the result of their homing behaviour combined with monsoonal alternation between aridity and flooding over recent and geological time scales since the Miocene period.