Conflicts with fisheries are the major threat to South American sea lions (Otaria flavescens). The understanding of the gap between perceived economic impact by the fishermen and actual impact on the activity is crucial to avoid retaliations to the species. This is the first study conducted in Brazil that simultaneously assessed these both aspects of this complex issue. To assess the fisheries economic revenue and economic loss caused by sea lions, we conducted 58 onboard surveys between 2011 and 2012, covering 161 fishing operations. To assess socio-economic characteristics, perceptions of economic loss caused by the sea lions, and temporal changes in the fishing activity, we interviewed one hundred fishermen. Onboard observations indicated that sea lions interact with fishing boats throughout the year. This finding is in agreement with the reports of most fishermen (69%) who believed that this interaction occurs every day and the species is always present during fishing operations (80%). On the other hand, while onboard surveys revealed that only 3% of loss in the annual productivity was due to predation by sea lions (~US$ 1931.00 out of total catch of US$ 62,279.00), fishermen assigned a disproportionate economic loss to sea lions: 88% of the respondents believed that each sea lion consumed around 100 kg of fish per interaction. This misperception and consequent conflict would decrease if fishermen were aware of the actual losses caused by sea lions. To mitigate conflict, an effective communication strategy and open dialogue between fishermen and the local marine Consulting Council is recommended.