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Infection by Caryospora cheloniae has been reported to be responsible for green turtle strandings with high morbidity and mortality rates worldwide. Although studies have already shown the pathogenesis of these infections, many aspects of this protozoan are still poorly understood, including their life cycle and infection dynamics in free-living sea turtle populations. Due to the lack of information about the infection by this protozoan in sea turtles in Northeastern Brazil, our study aims to describe Caryospora sp. infection and its pathological findings in free-living Chelonia mydas found on the north coast of the Bahia state. Between 2018 and 2019, 64 specimens of green turtles were necropsied in partnership with Fundação Projeto Tamar; among these, 10 (1.56%) had oocysts morphologically compatible with Caryospora cheloniae in the evaluation of fecal samples and histopathological examination of intestinal samples. The infected animals were juvenile green turtles that were found stranded on the beaches of the north coast of Bahia. The pathological findings were restricted to the lower gastrointestinal tract, with different presentations and intensities. About 70% of the animals with coccidial infection exhibited erosive and ulcerative fibrinous enteritis. This is the first report of coccidiosis in green turtles on the north coast of Bahia., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)