Remote rural fishing communities in Eastern Indonesia are in danger of suffering livelihood loss as a result of declining marine resources and increasing social and economic pressures, but also through management decisions which are often based solely on biological data and do not take into account the needs of local fishers. We present preliminary data from an interdisciplinary investigation of East Indonesian shark fisheries and their significance to fishing communities. Using methodologies from the natural and social sciences, we aim to identify options for shark management in the Arafura, Halmahera and Seram Seas, where shark fisheries are presumably extensive but remain largely unregulated and unreported. Through DNA barcoding of dried fin samples and by engaging shark fishers in the collection of biological data from captured sharks, we obtain vital baseline data on shark populations in fishing grounds around Halmahera in Northern Maluku and Raja Ampat, a shark and ray sanctuary in West Papua Province. Through participant observation, focus group discussions and semi-structured interviews we assess ecosystem awareness, shark fishing traditions, local knowledge and livelihood requirements in three fishing communities exploiting those fishing grounds. This study identifies the challenges of shark management in Eastern Indonesia, where current conservation initiatives threaten to displace fishing effort and negatively impact on the livelihood security of remote fishing communities. We address the contribution of this interdisciplinary, longitudinal approach to shark management in light of the biological, economic and social factors affecting a fishery that provides an important source of income but is increasingly contested globally