The seasonal ecological response of microzooplankton in the southeastern Arabian Sea is presented. During the spring intermonsoon period (March), stratification and depletion of nitrate in the surface waters (nitracline was at 60 m depth) caused low integrated chlorophyll a (av. 19 ± 11.3 mg m-2) and primary production (av. 164 ± 91 mgC m-2 d-1). On the other hand, nutrient enrichment associated with coastal upwelling and river influx during the onset and peak summer monsoon resulted in high integrated chlorophyll a (av. 21 ± 6 mg m-2 and av. 29 ± 21 mg m-3 respectively) and primary production (av. 255 ± 94 mg Cm-2 d-1 and av. 335 ± 278 mgC m-2 d-1 respectively). During all three periods, diazotropic cyanobacterium Trichodesmium erythraeum dominated in the nutrient depleted surface waters. A general increase in abundance of larger diatoms was evident in the surface waters of the inshore region during monsoon periods. The microzooplankton abundance was found to be significantly higher during the spring intermonsoon (av.241 ± 113 x103 ind.m-2) as compared to onset of summer monsoon (av. 105 ± 89 x103 ind.m-2) and peak summer monsoon (av.185 ± 175 x103 ind.m-2). Microzooplankton community during the spring intermonsoon was numerically dominated by ciliates while heterotrophic dinoflagellate was the dominant ones during the monsoon periods. The high abundance of ciliates during the spring intermonsoon could be attributed to the stratified environmental condition prevailed in the study area which favors high abundance of smaller phytoplankton and cyanobacteria, the most preferred food of ciliates. On the other hand, the dominance of heterotrophic dinoflagellates during the monsoon periods could be linked to their ability to graze larger diatoms which were abundant during the monsoon periods. The overall results show low abundance of microzooplankton in the eastern Arabian Sea during the monsoon periods mainly due to a decline in ciliates abundance. This decline during the monsoon periods could be the result of (a) low abundance of smaller phytoplankton and (b) high stock of mesozooplankton predators (av. 245 ml 100 m-3).