Industrial-scale harvest of species at risk of extinction is controversial and usually highly regulated on land and for charismatic marine animals (e.g. whales). In contrast, threatened marine fish species can be legally caught in industrial fisheries. To determine the magnitude and extent of this problem, we analyze global fisheries catch and import data and find reported catch records of 91 globally threatened species. Thirteen of the species are traded internationally and predominantly consumed in European nations. Targeted industrial fishing for 73 of the threatened species accounts for nearly all (99%) of the threatened species catch volume and value. Our results are a conservative estimate of threatened species catch and trade because we only consider species-level data, excluding group records such as ‘sharks and rays.’ Given the development of new fisheries monitoring technologies and the current push for stronger international mechanisms for biodiversity management, industrial fishing of threatened fish and invertebrates should no longer be neglected in conservation and sustainability commitments.

By‐catch is the most significant direct threat marine megafauna face at the global scale. However, the magnitude and spatial patterns of megafauna by‐catch are still poorly understood, especially in regions with very limited monitoring and expanding fisheries. The Indian Ocean is a globally important region for megafauna biodiversity and for tuna fisheries, but has limited by‐catch data. Anecdotal and scattered information indicates high by‐catch could be a major threat. Here, we adapt a Productivity Susceptibility Analysis tool designed for data‐poor contexts to present the first spatially explicit estimates of by‐catch risk of sea turtles, elasmobranchs, and cetaceans in the three major tuna fishing gears (purse seines, longlines, and drift gill nets). Our assessment highlights a potential opportunity for multi‐taxa conservation benefits by concentrating management efforts in particular coastal regions. Most coastal waters in the northern Indian Ocean, including countries that have had a minimal engagement with regional management bodies, stand out as high risk for fisheries interactions. In addition to species known to occur in tuna gears, we find high vulnerability to multiple gear types for many poorly known elasmobranchs that do not fall under any existing conservation and management measures. Our results indicate that current by‐catch mitigation measures, which focus on safe‐release practices, are unlikely to adequately reduce the substantial cumulative fishing impacts on vulnerable species. Preventative solutions that reduce interactions with non‐target species (such as closed areas or seasons, or modifications to gear and fishing tactics) are crucial for alleviating risks to megafauna from fisheries.