Australian carp gudgeons (Hypseleotris spp.) of the Murray–Darling basin are a species complex including sexually reproducing taxa and unisexual hybrid lineages that reproduce via hybridogenesis. Unisexual fish require gametes of a sexual species to propagate themselves and can be regarded as ‘sexual parasites’ capable of driving closed populations to extinction. Metapopulation dynamics have been proposed as a mechanism that could facilitate coexistence between a sexual parasite and its ‘host’. This study evaluates whether patterns of spatial genetic variation are compatible with metapopulation dynamics for a sexually reproducing member of the carp gudgeon complex (Hypseleotris sp. HA), in the Granite Creeks system of central Victoria. Genetic differentiation of fish among all study sites was accommodated by a model of migration-drift equilibrium using decomposed pairwise regression analysis. Given that the population was divided into discrete patches in the form of refugial waterholes during the time of this study, we infer that spatially constrained source–sink metapopulation dynamics may be responsible for producing this pattern. It is therefore possible that metapopulation dynamics contribute to coexistence in the Granite Creeks carp gudgeon hybridogenetic system, and further analysis is required to determine the relative importance of environmental versus demographic factors towards patch extinction.