Pelagic gillnet (driftnet) fisheries account for some 34% of Indian Ocean tuna catches. We combined published results from 10 bycatch sampling programmes (1981−2016) in Australia, Sri Lanka, India and Pakistan to estimate bycatch rates for cetaceans across all Indian Ocean tuna gillnet fisheries. Estimated cetacean bycatch peaked at almost 100 000 ind. yr −1 during 2004−2006, but has declined by over 15% since then, despite an increase in tuna gillnet fishing effort. These fisheries caught an estimated cumulative total of 4.1 million small cetaceans between 1950 and 2018. These bycatch estimates take little or no account of cetaceans caught by gillnet but not landed, of delayed mortality or sub-lethal impacts on cetaceans (especially whales) that escape from gillnets, of mortality associated with ghost nets, of harpoon catches made from gillnetters, or of mortality from other tuna fisheries. Total cetacean mortality from Indian Ocean tuna fisheries may therefore be substantially higher than estimated here. Declining cetacean bycatch rates suggest that such levels of mortality are not sustainable. Indeed, mean small cetacean abundance may currently be 13% of pre-fishery levels. None of these estimates are precise, but they do demonstrate the likely order of magnitude of the issue. Countries with the largest current gillnet catches of tuna, and thus the ones likely to have the largest cetacean bycatch are (in order):

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Indonesia harbours a high diversity of cetaceans, yet effective conservation is hampered by a lack of knowledge about cetacean spatial distribution and habitat preferences. This study aimed to address this knowledge gap at an adequate resolution to support national cetacean conservation and management planning. Maximum Entropy (Maxent) modelling was used to map the distribution of 15 selected cetacean species in seven areas within Indonesian waters using recent cetacean presence datasets as well as environmental predictors (topographic and oceanographic variables). We then combined the individual species suitable habitat maps and overlaid them with provincial marine spatial planning (MSP) jurisdictions, marine protected areas (MPAs), oil and gas contract areas, and marine traffic density. Our results reflect a great heterogeneity in distribution among species and within species among different locations. This heterogeneity reflects an interrelated influence of topographic variables and oceanographic processes on the distribution of cetacean species. Bathymetry, distance to-coast and the − 200m isobaths, and chlorophyll-a concentration and sea surface temperature were important variables influencing distribution of most species in many regions. Areas rich in species were mainly related to coastal areas or insular-reef complexity, representing high productivity and upwelling-modified waters. Although some important suitable habitats currently fall within MPAs, other areas are not and overlap with oil and gas exploration activities and marine traffic, indicating potentially high risk areas for cetaceans. The results of this study can support national cetacean conservation and management planning, and be used to reduce or avoid adverse anthropogenic threats. We advise to consider currently unprotected suitable cetacean habitats in MPA and MSP development.