Indonesia has the world’s largest shark fishery, but very little locally relevant information is available on catch statistics or life history characteristics of targeted species. This poses major challenges for fisheries management and shark conservation in the region, particularly in the more remote coastal communities of Eastern Indonesia. Shark fishers from three coastal communities were interviewed and trained in data collection in their fishing grounds in the Seram, Aru-Arafura and Timor Seas. Of the over 30 species recorded by the fishers, we assessed ten species based on criteria including proportion of total catch, high intrinsic vulnerability to fishing pressure, and market and conservation value. Using a combination of fishers’ data and published life history characteristics, we estimated the intrinsic rate of population growth to evaluate the relative vulnerability of each species, and compared the observed size structure with established fisheries reference points. The interviews revealed that the fishers generally perceived sharks in their fishing grounds to be declining in numbers and size. Our study found that the fishery is catching several high risk species, such as hammerheads and guitarfish, with catches predominantly comprised of immature individuals and a high level of fishing mortality. Involving fishers in data collection and interpretation provided data and information in regions with low management and research capacity. Additionally, close collaboration with the fishers provided fundamental insights into the circumstances that shape fishers’ decision-making and the ecological and socio-economic requirements that must be addressed for management initiatives to be effective