We investigate the population genetic structure of the declining western subspecies of the purple-crowned fairy-wren (Malurus coronatus coronatus) in order to guide conservation management recommendations for this riparian habitat specialist. Our analysis of multilocus microsatellite data, from 79 individuals sampled from across the species’ range, indicates that M. c. coronatus occurs as genetically differentiated subpopulations that correspond to catchment boundaries or expansive gaps in habitat along waterways. The genetic similarity of large populations of fairy-wrens on four catchments (Fitzroy, Durack, Drysdale and Victoria) indicates widespread recent gene flow, whereas the high genetic distinctiveness of the Bindoola and Isdell catchments may reflect the current geographic isolation of these smaller populations. Genetic differentiation of these smaller geographically isolated populations affirms the negative effect that habitat degradation and fragmentation can have on population connectivity. A regional-scale approach to conservation with a focus on preventing degradation and enhancing connectivity may be critical to safeguard the persistence of M. c. coronatus subpopulations.