Reductions in genetic diversity and genetic connectivity have been documented in some predatory bird species in response to anthropogenic habitat fragmentation. The Southern Boobook (Ninox boobook) is the most common and widely-distributed owl in Australia but declines in abundance have been observed across its range. We used polymorphic microsatellite loci to investigate landscape-scale patterns of genetic variation and spatial genetic structure in boobooks from a variety of fragmented landscape types and relatively undisturbed landscape types across Western Australia. The maximum distance between collection locations of genetic samples was 1391 km. Indirect estimates of connectivity inferred from these genetic data were complemented by direct estimates of post-breeding dispersal of juvenile boobooks gathered from banding data resulting from this and other studies across Australia. We found high genetic diversity in microsatellite markers, weak spatial genetic structuring and no evidence of genetic erosion associated with inbreeding in heavily fragmented landscapes. Bayesian modelling, spatial autocorrelation analysis and principal coordinates analysis suggested a single large panmictic population across all areas sampled. Within the heavily fragmented landscape of an extensive urban area, band re-sightings and recoveries substantiate the considerable capacity of juvenile boobooks to disperse across areas far greater than the distance between patches. We hypothesise that the genetic homogeneity observed in this species is a consequence of long-distance dispersal capacity in addition to their ability as habitat and dietary generalists to make use of highly altered habitats.