We analysed the fishermen’s perceptions on the South American sea lions (Otaria flavescens) and its interactions with the local fishery close to the Wildlife Refuge of Ilha dos Lobos, a marine protected area in southern Brazil. Sea lions prey upon the same resources targeted by the fishermen. They repeatedly hunt on the nets and consequently damage them. In response, fishermen persecute sea lions. However, in conflicts with high-profile animals, the perceived damage often exceeds the actual evidence. Results from 100 interviews revealed that fishermen’s perception of damage and their attitudes were affected by age, hierarchical position in the crew, if fishing was the only source of income, and level of formal education. Greater perception of damage and more negative attitude were found among older, less educated sailor fishermen who had no other source of income besides fishing. The average fisherman had a relatively good knowledge about sea lions, but also a negative attitude towards them. We recommend actions addressing these negative attitudes through environmental education, with emphasis on adjusting exaggerated perceptions of impact and the potential of the species for wildlife tourism, as a vital step towards the conciliation of sustainable fisheries and O. flavescens conservation in the Brazilian coast.