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Flying fish is an important economic fish in Makassar Strait that become fishermen target, especially their roes, their populations were indicating high exploitation pressures. Gill nets were the dominant fishing gear with the net mesh size were varying depending on the season. The aim of the study was to compare the capture capability of gill nets with 3 different mesh sizes. The study used a field experimental approach to obtain gill nets selectivity on flying fish catch. Variables observed include different net mesh size, number, weight and fork length of flying fish catches. Data were analyzed using variance test to compare between treatments. The fish catch data shows that the highest fish catches was 1.25 inches, and the rest 1 and 1.5 inches. The results of the statistical test show that the number of catch fish is highly significant different (P<0.05) on the mesh size of 1 inch, 1.25 inches and 1.5 inches. There were an indication that flying fishes getting smaller, which is indicated by most of fish catches pass the length at the first maturity size. Gill net of 1.25 inch mesh size should be used to maintained the sustainability of flying fish population.