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1. Climate change is emerging as one of the greatest threats to coral reef ecosystems. Climate-induced warming events trigger coral bleaching and mortality, which can indirectly affect coral reef fishes. Managing fisheries across coral mortality events is expected to influence the persistence of species and reef recovery potential. The most common management recommendation has been to prohibit fishing using fisheries closures, but this response often has limited support from resource users. 2. Here, we explore an alternative of managing fishing gear commonly used in artisanal coral reef fisheries. We examined fisheries landing data from 15 sites in Papua New Guinea and Kenya to explore whether or how specific gears select for: (i) species that depend on coral reefs for feeding or habitat and are likely to be susceptible to the loss of coral, and (ii) different functional groups of fishes. 3. Only 6% of the fishes targeted by fishers were susceptible to the immediate effects of coral mortality; however, loss of habitat structure following coral mortality is expected to affect 56% of targeted species. 4. Importantly, 25% of target species had feeding characteristics (i.e. reef scrapers/excavators and grazers) that contribute to the recovery of coral reef ecosystems, and gears differed considerably in catches of these species. 5. Spear guns and traps target a high proportion of species likely to be affected by bleaching and key for the recovery of corals. These gears are strong candidates for management restrictions in reefs with high coral mortality. In contrast, line fishing catches the lowest proportion of susceptible and recovery-enabling species and is preferential for increasing recovery rates on coral reefs. 6. Synthesis and applications. Fisheries managers will require a range of tools to meet the novel challenges posed by climate change. This study presents a way to help reduce the negative impacts of climate change and potentially increase resilience of marine ecosystems by managing fishing gear. Specific gears used by artisanal fishers differentially target fish functional groups. In the coral reefs that we studied, traps and spear guns targeted a high proportion of species highly susceptible to coral mortality and critical to coral reef resilience through their top-down control. Given that full fisheries closures are not always practical, selectively banning or restricting fishing gears is a potentially powerful tool for reducing the detrimental ecosystem effects of climate change disturbances. © 2008 British Ecological Society.