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Manta rays are marine planktivorous elasmobranchs that are distributed worldwide and highly susceptible to overexploitation. Although they are legally protected in Brazil since March 2013, incidental and intentional captures still occur. The sharp population decline following the intensification of targeted fisheries and bycatch highlights the urgent need of manta ray protection. This study provides information on several threats to manta rays (Mobula birostris and M. cf. birostris) in Brazil, including the frequency and geographic extent of the occurrences and their fishing and entanglement with fishing gear. We analysed photo/video records, and the scientific literature reporting mobulids incidence and focused on events of entanglement in fishing gear, intentional and incidental caught of manta rays, obtained from 2000 to 2020. From a total of 270 records of manta rays’ occurrences, 70 displayed wounds from anthropogenic activities, including 29 lethal records. Most of the injured individuals were recorded in the State of São Paulo (31.4%; n = 22), followed by Pernambuco (20.0%; n = 14), Rio de Janeiro (10.0%; n = 7), Bahia (8.6%; n = 6), Rio Grande do Norte (7.1%; n = 5), and Espírito Santo (5.7%; n = 4). Despite outnumbered, all manta rays’ occurrences in the states of Rio Grande do Norte, Ceará, Sergipe, Pará, Piauí and Santa Catarina showed individuals either captured by fishers, with body scars or dragging fishing artefacts. The majority (61.4%) of injured individuals were recorded after the national protected status was implemented to the family Mobulidae, and all injuries observed were consequences of anthropogenic action. Our results highlight the diverse sources of threat and injuries patterns for manta rays in the nationwide territory and underscore the urgent need for monitoring fishing impacts and promoting effective enforcement of the national regulation for the protection of manta rays in Brazil.