This study on surface Zooplankton examined monthly samples for two consecutive years (2013 - 2014) collected at the sea surface from two locations simultaneously; Muscat in the Sea of Oman and Salalah in the Arabian Sea. The general objective was to investigate the changes in zooplankton communities in response to the seasonal forcing of the monsoon regime experienced differently in the Sea of Oman and the Arabian Sea. This main goal will be achieved through the following specific objectives: 1) Describe and characterize the zooplankton community in two contrasting water masses, and 2) Characterize the seasonal changes in zooplankton community structure in terms of abundances and biomass. The species composition of the zooplankton communities varied significantly between Salalah and the Muscat. The two communities were most similar during winter at the time of northeast monsoon and show the largest differences (dissimilarity) in composition during summer at the time of southwest monsoon. The seasonal changes in community structures were most significant for copepods and calanoid copepods and less significant for non-copepods suggesting that the relative abundances of the three orders of copepods (Calanoida, Cyclopoida, and Harpacticoida) responded to the seasonal environmental changes. Out of 91 species, only 17 in Muscat and 20 in Salalah represented more than 90% of the total zooplankton abundance. Copepods and Meroplankton had a distinct and clear pattern in Salalah but there was no such obvious pattern in Muscat. During periods of lack of food, certain zooplankton species, such as Temora turbinata and Penilia avirostris in the Muscat, and Oithona spp. in Salalah, expanded their range of feeding selection to include smaller phytoplankton cells and ciliates through the microbial loop and, thus, defies the concept of zooplankton paradox. No variation in the normalized biomass spectra in both locations (-0.88 in the Muscat, and -0.87 in Salalah). There is a seasonality in the total biomass of zooplankton in both locations. The highest peak of biomass in both locations occurred in southwest monsoon (Summer). However, Meroplankton showed a seasonality in Salalah with a significant drop during southwest monsoon. The species with the highest biomass in the Muscat seem to be adapted to microbial loop exploitation.