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Fishery data collected from the Reunion Island and Sechelles pelagic longline fisheries (targeting swordfish and tuna) between 2004 and 2015 was used to propose depredation indicators and to assess depredation levels in these fisheries. The interaction rate (depredation) was significantly higher for sharks compared to toothed whales in both fisheries. However, there was a higher depredation per unit effort from toothed whales compared to sharks indicating the impact was more significant. The gross depredation rate in the Seychelles fishery was 18.3%. A slight increase in the gross depredation rate was seen over time in the Reunion Islands fishery (4.1% 2007-2010 and 4.4% in 2011-2015). These indicators were used to estimate the economic loss to these fisheries from depredation events. For the Reunion Island fishery the economic loss was 0.09 EUR/hook and 0.86 EUR/hook for the Seychelles. The results suggest a southward decreasing tooth whale and shark depredation gradient. The depredation levels in the Seychelles are some of the highest in the world and may suggest a 'hot spot' of interactions between toothed whales and pelagic longlines.