The five sea turtle species occurring in Brazilian waters are susceptible to threats, including incidental catches by fisheries. Studies on incidental captures in fishing gears are the main focus of several conservation actions due to high sea turtle fishery mortality worldwide. This study provides the first evaluation of incidental sea turtle catches by industrial bottom trawl fisheries operating in Brazilian waters. Four twin-trawler vessels were monitored between July 2010 and December 2011 by captains who voluntarily completed logbooks. Forty-four turtles were captured during the 1996 tows (8313 fishing hours), resulting in a catch of 5.3 ± 0.8 turtles per 1000 h per unit effort. Captured species included the loggerhead turtle (Caretta caretta, 22 individuals), olive ridley turtles (Lepidochelys olivacea, 21 individuals) and one green turtle (Chelonia mydas). Water depth was the only variable that significantly affected sea turtle captures according to Generalized Linear Models. The capture rates reported in this study ranked sixth in relation to other published studies of similar fisheries occurring worldwide. Considering the importance of this region for sea turtles, the increasing evidence of sea turtle mortality and the goals of the National Action Plan for Conservation of Sea Turtles in Brazil, it is essential to identify the main threats towards these animals and propose mitigating solutions to reduce sea turtle mortality induced by fishing activities. This study provides results that may guide future research and goals in meeting sea turtle conservation strategies.