The apparent population recovery of giant otters during the last ten years in the Amazon and Orinoco basins in Colombia is creating serious conflicts between local fisheries and this species. This paper presents evidence of conflicts in the Orinoco, Meta and Bita rivers in the Orinoco basin, in the Inírida and Guaviare rivers, and in the Caquetá, Putumayo and Amazon rivers in the Amazon region. In most cases, fishermen are killing giant otters or are asking the government authorities to take action to reduce their numbers. Preliminary evaluations of giant otter diets indicated little competition with local fisheries. However, areas with more intense conflicts corresponded to regions with strong fishing pressure and bad management practices. We conclude that interference with fisheries by giant otters is relatively low but it is necessary to undertake management of the fisheries in the region to avoid perceived conflicts.