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Anthropogenic activities affect water quality and biological resources in bays such as zooplankton community. A survey on the zooplankton in Manila Bay was done from January to December 2013 in relation to physico-chemical parameters.Temperature and salinity in the bay showed uniform spatial patterns. Mean DO concentrations in the bay ranges from 2.79-6.25 mg/L, the lowest value was recorded in station 14 in the month of July with a value of 1.01 mg/L. Mean concentrations of nitrate, phosphate, nitrite, silicate ranges from 0.0265-8.3902 μM, 0.0135-0.2573 μM, 0.1385- 0.8396 μM, and 5.4887-53.2027 μM respectively. Arthropods, consist mainly of copepods, dominated the zooplankton community in the bay. High concentrations were observed in the eastern and southern part of the bay. Copepod nauplii, calanids and Oithona sp. were among the dominant species. Redundancy Analysis revealed that salinity, temperature, dissolved oxygen, phosphate and nitrate have positive correlation with zooplankton.