This research was conducted to identify population structure and reproduction aspect of big eye tuna (Thunnus obesus) in west off Sumatra and south off Java and Nusa Tenggara of Indian Ocean. The sample of fish was collected from catch landed by fishermen. The fish was caught from the Indian Ocean during 2010. Analysis of population structure was done by using of histology technique of fish genetic and reproduction. Result showed that population structure of the big eye tuna in Indian Ocean consisted of two different sub populations namely sub population in west off Sumatra and another one is sub population in south of Java and Nusa Tenggara waters. The most of bigeye tuna catch (about 39%) was categorized as immature fish with Gonad Somatic Index stage I. The immature fish was mostly found in west off Sumatra waters. While the catch in south off Java and Nusa Tenggara waters was mostly categorized as mature fish. It was indicated that south off Java and Nusa Tenggara waters was as spawning ground of the big eye tuna.