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Incidental capture by fisheries is one of the principal threats to sea turtles. This study analysed spatial and temporal patterns of sea turtle bycatch, and estimated the direct initial mortality rate of these animals, in the industrial double‐rig‐bottom trawl fishery in south‐eastern Brazil. This is also the first attempt to relate bycatch/at‐sea mortality in bottom trawling to stranded turtles found along the adjacent coast.The fishery was monitored from October 2015 to April 2018 through data collected voluntarily by the captains of eight industrial double‐rig trawlers. Two hundred and one sea turtles were captured during 9362 tows (43,657.52 trawling hours), resulting in a catch per unit effort (CPUE) of 0.0025 ± 0.0032 turtles h−1 with a standard net of 30.5 m headrope, with no significant difference between the estimated CPUEs for licensed shrimp and demersal fish trawlers.Caretta caretta (52.24%) and Lepidochelys olivacea (38.81%) were the most frequently captured species. According to Generalized Linear Models, C. caretta bycatch was significantly higher during winter, at lower latitudes (−24° to −23°) and higher longitudes (−42° to −40°), while the L. olivacea bycatch was significantly higher at higher latitudes (−23° to −21°). The direct initial mortality rate of sea turtles in the shrimp trawlers was 7.65 ± 3.85%. However, none of the dead individuals subsequently released with plastic tags (n = 10) were found stranded on the coast. Mortality was not significantly related to the depth or duration of the trawling.The results of this study suggest the need for improvements to the current management of the bottom trawl fishery in Brazil, moving from a species‐based to a spatial and seasonal‐based approach. There is also a need to develop turtle excluder devices adapted to local fishing conditions. [ABSTRACT FROM AUTHOR]