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The incidental capture of cetaceans in fisheries threatens several species with extinction and represents a global conservation challenge. In order to assess the impacts of bycatch on dolphins in a north-western Australian trawl fishery, I (i) examined bycatch reported in skippers’ logbooks and independent observer data; (ii) applied genetic methods to estimate dolphin population structure and connectivity; and (iii) conducted an aerial survey to estimate dolphin abundance across the fishery, simultaneously undertaking boat-based photo-identification to infer fidelity to the fishery. From 2003-2009, between 180 and 366 dolphins were caught across all management areas, depths and seasons. Independent observers reported more than double the dolphin bycatch reported in skippers’ logbooks. Significant predictors of dolphin bycatch were fishing vessel, time-of-day and whether nets included Bycatch Reduction Devices (BRDs). Genetic evidence showed one panmictic population of trawler-associated common bottlenose dolphins (Tursiops truncatus), but isolation from all adjacent, coastal populations of Indo-Pacific bottlenose dolphins (T. aduncus). Abundance was estimated at 2,000-3,000 T. truncatus across 25,880 km2. While the lack of correction factors for availability bias mean this is likely an underestimate, it is lower than previously thought. Trawler-associated individuals were photographically and genetically matched over periods of days to years. Recent skippers’ logbook data suggest dolphin bycatch rates have increased since the BRDs were introduced. These results indicate that (i) only a considerable reduction in trawling effort is likely to reduce dolphin bycatch; (ii) the impacted population does not recruit from the adjacent coastal populations; and (iii) the number of dolphins interacting with trawlers is fewer than expected. The chronic bycatch of this protected species may affect the dolphin population’s conservation status. As a consequence, the classification of acceptable limits of bycatch requires revision in light of these first estimates of the abundance and fidelity of bottlenose dolphins interacting with the Pilbara Trawl Fishery.