| Summary: | <p>Abstract</p> <p>Background</p> <p>The territorial fishing zones of Australia and Indonesia are contiguous to the north of Australia in the Timor and Arafura Seas and in the Indian Ocean to the north of Christmas Island. The area surrounding the shared boundary consists of a variety of bio-diverse marine habitats including shallow continental shelf waters, oceanic trenches and numerous offshore islands. Both countries exploit a variety of fisheries species, including whaler (<it>Carcharhinus spp</it>.) and hammerhead sharks (<it>Sphyrna spp</it>.). Despite their differences in social and financial arrangements, the two countries are motivated to develop complementary co-management practices to achieve resource sustainability. An essential starting point is knowledge of the degree of population subdivision, and hence fisheries stock status, in exploited species.</p> <p>Results</p> <p>Populations of four commercially harvested shark species (<it>Carcharhinus obscurus</it>, <it>Carcharhinus sorrah</it>, <it>Prionace glauca</it>, <it>Sphyrna lewini</it>) were sampled from northern Australia and central Indonesia. Neutral genetic markers (mitochondrial DNA control region sequence and allelic variation at co-dominant microsatellite loci) revealed genetic subdivision between Australian and Indonesian populations of <it>C. sorrah</it>. Further research is needed to address the possibility of genetic subdivision among <it>C. obscurus </it>populations. There was no evidence of genetic subdivision for <it>P. glauca </it>and <it>S. lewini </it>populations, but the sampling represented a relatively small part of their distributional range. For these species, more detailed analyses of population genetic structure is recommended in the future.</p> <p>Conclusion</p> <p>Cooperative management between Australia and Indonesia is the best option at present for <it>P. glauca </it>and <it>S. lewini</it>, while <it>C. sorrah </it>and <it>C. obscurus </it>should be managed independently. On-going research on these and other exploited shark and ray species is strongly recommended. Biological and ecological similarity between species may not be a predictor of population genetic structure, so species-specific studies are recommended to provide new data to assist with sustainable fisheries management.</p>
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