For centuries Indonesian fishers have harvested marine organisms from waters off north Australia. This has continued under an Australian and Indonesian Memorandum of Understanding (MOU), signed in 1974, that allows traditional Indonesian fishers access to 48,000 km2 off north-western Australia. In this area, known as the MOU Box, Indonesian fishers fish for sedentary organisms, finfish, and sharks which are believed to have come under greater fishing pressure over the past decade. Despite concern, and in contrast to other Australian shark fisheries, little work has been done quantifying catch composition, a pre-requisite for effective fisheries management. Establishing the catch composition in this fishery is challenging because the catch can only be inspected post capture and is retained as parts, such as fins. In this project novel techniques were used to identify all sharks on nine traditional Indonesian vessels operating in the MOU Box. Photos and tissue samples were collected from 152 dorsal fins and were identified to species using expert visual identification and DNA methods. Sixteen different species belonging to the families Carcharhinidae (Whalers) and Sphyrnidae (Hammerheads) were identified. The most abundant species were Sandbar Shark Carcharhinus plumbeus and Tiger Shark Galeocerdo cuvier, representing 43.4% and 29.6% of the total catch, respectively (from a catch with an estimated weight of 10.5 tonnes). Furthermore, we tested two semi-automated fin identification methods, developed for field use by non-fin experts. These methods varied in success, with the morphometric identification technique achieving 69% accuracy and the FAO iSharkFin program only 29% accuracy. This project provides fundamental catch information for the management of northwest Australian shark fisheries, both in and outside the MOU Box. Our study demonstrates the value of validating semi-automated methods using diagnostic expertise and also highlights the difficulties associated with applying these methods to varying assemblages. If adopted more widely, the techniques used in this study can be used to improve the accuracy of global elasmobranch fisheries data.