Tuna fishes are among the most important commercial fishes used in Iran fish canning industry. The precooking of fish is one of the important stages of producing liquid wastes in canning factories. The liquid waste by-product obtained at this stage contains different amounts of fat removed from the fish. Fish oil includes some polyunsaturated fatty acids with long chains (PUFA), especially EPA, DHA and AA. The oil obtained from the liquid waste of cooking autoclaves of two tuna fishes, Katsuwonus pelamis and Thunnus albacares, were investigated in terms of iodin value, acidity, peroxide, oil and cooking liquid waste yield. The total yield of liquid waste showed a significant increase in Thunnus albacares (22.5%), as compared with Katsuwonus pelamis (20.4%), (p˂0.05). The oil of Thunnus albacares (1.55%) was found to be more than that of Katsuwonus pelamis (0.81%), (p˂0.05).In terms of iodin value, the oil of Katsuwonus pelamis cooking liquid waste showed higher amounts and in terms of peroxide, Thunnus albacares showed higher values (p˂0.05).The predominant fatty acids in tuna liquid waste by-product were Palmeticacid (C16: 0; 21.12%, 24.11%), oleicacid (C18: 1c 9; 15.46%, 12.35%), and docosahexaenoic acid (C22: 6 3DHA; 23%, 23.15%), for Katsuwonus pelamis and Thunnus albacares, respectively. The highest PUFA, and PUFA/SFA ratio was found in Katsuwonus pelamis and the highest SFA was found in Thunnus albacares. Finally, due to the higher unstauration degree and also, the lower peroxide in equal weights, the oil obtained from Katsuwonus pelamis is deemed to be more suitable, but in the industrial scale, because of the higher yield of the oil extracted from Thunnus albacares, this tuna fish is more preferable.