Aquifers harbor a unique and highly specialized fauna (stygofauna). The stygofauna often comprise short-range endemics, making them particularly vulnerable to extinction. In Australia, the demand for groundwater is ever-increasing, resulting in a conflict of interest concerning the management and conservation of these ecosystems. Knowledge of the levels of connectivity for groundwater taxa is needed to develop appropriate management strategies. We used next-generation sequencing to develop a panel of 10 polymorphic microsatellite markers for the Parabathynnelidae, an ancient group of groundwater invertebrates. These loci were amplified by PCR in 32 individuals from Wellington, New South Wales Australia. The number of alleles per locus ranged from 2 to 7, and observed and expected heterozygosities from 0.32 to 0.90 and 0.31 to 0.84, respectively. Five loci were successfully amplified in stygofauna taxa other than parabathynellids. These molecular markers will be a valuable resource for the conservation management of groundwater invertebrate populations.