Evidence of the presence of a group of sei whales (Balaenoptera borealis) detected around drifting fish aggregating devices (FADs) was provided by omnidirectional multi-beam sonar during a survey off the Seychelles (Indian Ocean). The short visit by the sei whales produced a significant change in the behaviour of the fish assemblage associated with the FAD. There was first a significant increase in fish density when the whales approached the FAD, then a marked decrease after the whales had moved away from the FAD. Furthermore, the fish density was still low, 3 h after the whales had left the FAD. We assume that the presence and behaviour of the sei whales led some of the fish initially associated with the FAD to move away from it. There has been a considerable increase in the use of drifting artificial FADs in the Indian Ocean in recent decades. The frequency of cetacean visits to drifting FADs in the Indian Ocean is unknown, but they may have a major impact on assemblages of pelagic fish species around FADs. The effect of marine mammals on FAD-associated fish could be relevant to the ecological trap theory (FAD acting as a trap for their associated fish) because of their impact on the dynamics of fish aggregation processes, through commensalism and/or predator–prey interactions.