The zooplankton diversity of Helleh estuary, Busheher, Persian Gulf, and its relationship with some characteristics of water quality was investigated. Samples were taken using plankton net (mesh size of 140 mm) with vertical towing from 5 fixed-stations in mid-season from summer 2011 to spring 2012 for one year period. The mean (±SE) of biodiversity indices of Simpson, Shannon-Wiener, and Margalef were, respectively 0.84±0.10, 3.01±0.20, and 1.90±0.10 in summer; 0.63±0.06, 2.20±0.20 and 1.87±0.08 in autumn; 0.73±0.04, 2.22±0.10 and 1.43±0.10 in winter; and 0.87±0.01, 3.44±0.30, and 2.38±0.30 in spring. The seasonal zooplankton similarity based on Jaccard’s and Sorensen’s coefficients were highest (0.61 and 0.76) for summer-autumn, 0.56 and 0.72 for autumn-spring while these value were lowest for winter-autumn (0.27 and 0.43) and spring-winter (0.30 and 0.47). In addition, there were significant correlation between zooplankton density with salinity, dissolved oxygen and chlorophylla, Simpson and Shannon-Wiener with temperature, and Margalef with pH.