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Sardinella lemuru is a dominant small pelagic fish (80-90%) caught by purse seiner in Bali Strait, while the remaining 10-20% consist Decapterus spp., Euthynus affinis, and others. This composition typically varies seasonally, whereas Southeast monsoon season was dominated by S. lemuru, while Northwest monsoon season replaced by Decapterus spp. and E. affinis. Fishing trend in the last 14 years indicated regime shift with the shifting in species composition by a seasonal into the inter-annual due to global climate change, such as El Niño and La Niña 2006 was indicated a cold period of water temperature, which is triggered by the El Nino and positive Indian Ocean Dipole (pIOD). In this cold period, the S. lemuru reached peak of fishing, otherwise this fish disappear when warm period (strong La Niña) in 2010. When S. lemuru disappeared during warm period, it was substituted by Decapterus spp. Furthermore, as predatory fish of both small pelagic fishes, E. affinis always appear throughout the year. Understanding the species composition trend from seasonal to longer period is important for better strategy to manage fisheries of Bali Bali Strait in climate change era.