In a Sustainable Fisheries Strategy funded project, Fisheries Queensland investigated species composition of commercially retained and discarded shark from Queensland waters using a mitochondrial DNA (mtDNA) marker. It was determined that 44% of the commercial harvest was made up of a species complex including the Australian blacktip shark (Carcharhinus tilstoni) and the common blacktip shark (Carcharhinus limbatus). Despite having different biological characteristics, the two species are difficult to distinguish morphologically in the field. There is also the added difficulty in that there is evidence of hybridisation between the 2 species in their mtDNA (Ovenden et al. 2009). Single nucleotide polymorphism (SNP) markers were used to investigate this species complex across its Queensland distribution to look at the stock structure of each species and to explore whether hybridisation is an ongoing or historical relationship.