Information of vertical distribution of longline-hook species is important for the development of effective measures to mitigate bycatch, and very helpful for better understanding of the oceanic ecosystem structure and implementation of ecosystem-based fisheries management. Based on depth data of longline hook and capture hook position of pelagic species, collected by on board scientific observer in the southeast Pacific Ocean from September 2013 to January 2014, shoaling rate of longline hook and vertical distribution of 14 pelagic species were analyzed. The results showed that the relative shoaling rate range of longline hook was 8.9% - 17.1%, and the average relative shoaling rate was 13.5%. The depth ranges of 14 capture species were different. The species with the deepest depth was Opah (Lampris guttatus), and the species with the shallowest depth was skipjack (Katsuwonus pelamis). Except for yellowfin tuna (Thunnus albacares) and striped marlin (Tetrapturus audax), the mean depth and depth distributions of bycatch species were significantly different from that of the targeted albacore tuna (Thunnus alalunga).