Worldwide, fisheries bycatch remains one of the greatest immediate threats to cetacean populations. In Australia, short-beaked common dolphins are subject to bycatch mortality in 2 fisheries: the purse-seine fishery for sardines off central South Australia and the gillnet fishery for gummy sharks off southern Australia. The cumulative impact of bycatch from both fisheries on the dolphin population(s) in these regions are unknown. We used information from microsatellite markers and mitochondrial DNA to investigate population genetic structure and estimate contemporary migration rates in 332 biopsied and 15 stranded samples of common dolphins. Samples were collected from 11 locations along ~3500 km of coastline in southern and southeastern Australia. Bayesian and traditional analyses of population genetic structure revealed the presence of at least 6 management units of common dolphins, of which a minimum of 3 are potentially impacted by the 2 fisheries. These management units need to be managed separately for conservation purposes and for monitoring and mitigation of common dolphin fishery interactions off southern and southeastern Australia. We suggest that substructuring and migratory movements of common dolphins across these regions may be driven by spatial variations in oceanography, upwelling events and/or fish distribution. This study exemplifies how information on genetic substructuring in a neritic top predator can be valuable for fisheries bycatch management.