Globally, batoids face significant risk of extinction as a result of their K-selected life history strategies, paired with heavy commercial fishing for many species. The eastern shovelnose ray (Aptychotrema rostrata) faces substantial commercial fishing pressures in Australia, through high rates of bycatch in Queensland (QLD) and as a primary commercial target species in New South Wales (NSW). As with many batoids, there is a significant lack of research on population structure, leading to Aptychotrema spp. stock management regimes occurring at broad scales off the Australian east coast. Here we assessed the population structure of A. rostrata using single nucleotide polymorphisms (SNPs) from four sites in QLD and NSW. We detected evidence of a stock discontinuation, and that East Australian Current eddies off of Sydney may act as a genetic disjunction for A. rostrata. Further, mitochondrial DNA barcoding revealed batoid misidentification routinely occurring by fishers and fish markets in NSW, due to partial processing at sea (head removal). We recommend additional genetic investigations to determine the broader population structure of A. rostrata, along with management changes requiring rays to be landed whole, facilitating correct species identification and logbook reporting.