Zooplankton species composition has an important role in the food chain that can be used as water fertility indicator. It is strongly influenced by physical-chemical parameters, especially in the strait waters due to the discharge of freshwater as well as strong mixing. This study is aimed to analyze zooplankton distribution and diversity, and their correlation to physical-chemical parameters in the strait water of Maspari Island. The results showed that the zooplankton in the vicinity of Maspari Island can be grouped in 10 taxa, which are dominated by Calanoid (47%) and Harpacticoid (19%). Other taxa (e.g. Cyclopoid, Chaetognatha, Euphausia, Fish egg, Lensia, Ostracod, Brachyura and Polychaeta) only account for less than 10% for each taxa. The abundance of zooplankton obtained in range of 18 to 3205 Ind.L^-1, which is mainly found in a high Calanoid. Note that the distribution of zooplankton abundance in these waters found almost at all observation stations. Zooplankton diversity considered as low to moderate categories, with H’ index was 0.51<H’<1.66, and there was no type of zooplankton dominates (C<0.5). PCA Analysis shows the correlation between physical-chemical parameters with the zooplankton distribution and diversity is identifier by density, temperature, salinity, pH, current speed, nitrate, phosphate and turbidity.

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