Novel approaches are required to estimate the bycatch associated with artisanal fisheries. Foremost among these is the use of fisher knowledge (FK). An interview survey was conducted in ports along 2631 km of the Peruvian coast to assess the spatial patterns and bycatch rates of marine megafauna of the artisanal longline fishery and its relation with vessel characteristics and fishing operations. The survey allowed the assessment of 18% of the fleet, while only 1% of the Peruvian longline fleet has been monitored with on board observations in the past. The results indicate that big vessels (higher capacity, longline length and number of hooks) that travel long distances (average distance to coast: 123 nm) mainly catch turtles and show a small amount of seabird bycatches in north-central Peru. Small vessels especially impact turtles in southern Peru and near the coast (63 nm on average). Contrary to previously published information, which indicates a low level of cetacean bycatch in this fishery, a group of fishers reported more than 1000 cetaceans were incidentally captured in 2009. Using FK allowed to integrate different sources of information and scale the implications of artisanal fisheries in terms of bycatch. FK could further be used to help managers deal with the uncertainties in the dynamics of these generally data- poor social-ecological systems.