ABSTRACT: The narrow sawfish Anoxypristis cuspidata belongs to the most endangered family of chondrichthyan fishes, the sawfishes (Pristidae). This species has undergone significant declines in geographic range and abundance due to anthropogenic activities including fishing and habitat destruction. Very little is known of adult movements within its distribution. In order to better manage and protect this endangered species, understanding patterns of habitat use, connectivity and behaviour is important. Using a combination of partial mitochondrial sequences (control region [CR] and NADH dehydrogenase 4 [ND4]) and nuclear markers (microsatellites), this study assessed the genetic population structure of A. cuspidata in Australia and Papua New Guinea. Significant population structuring using mitochondrial DNA was found between the east Australian coast, Gulf of Papua and Gulf of Carpentaria (using concatenated CR and ND4 markers) (analysis of molecular variance [AMOVA], Φ_ST = 0.082, p = <0.001). In contrast, no population structure was evident across northern Australia using nuclear microsatellite loci (F_ST = 0.012, p = 1.000). Our results suggest that a combination of historic genetic drift, maternal natal philopatry and possible male-biased dispersal likely drive the genetic patterns observed. Given the endangered status and lack of knowledge for A. cuspidata, this study presents important insights that may be used to inform management efforts.