In this data article, we aimed to evaluate and compare the biological diversity and relative abundance of zooplankton communities in 3 different areas along the northern part of the Persian Gulf in 3 different seasons. Data showed that Centropages spp and Fish larvae were the highest and lowest species among the groups identified in summer in Lavare Saheli and Nakhle Taghi with relative abundances of 87% and 2.7% respectively. In winter, Cyphonautes larvae and Corycaeus spp. were the highest and lowest species in Kangan and Lavare Saheli with relative abundances of 57.1% and 1.88%, respectively. Also Decapoda larvae spp. and Gastropoda larvae were the highest and lowest species in spring in Kangan with relative abundances of 62.5% and 4.7% respectively. Data may serve as benchmarks for other groups working in the field of pollution control, aquatic ecosystem, and toxicology.

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