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Caspian Sea has gone under a lot of changes due to human influences and the unwanted presence of a ctenophora Menomiopsis leidyi which has greatly changed the structure of planktons in the last recent years. Therefore, this study was carried out in order to determine these changes in the zooplankton community. the Sampling was done in 8 transacts in Astara, Anzali, Sefidrood, Tonekaboun, Noushahr, Babolsar, Amirabad and Bandar Torkaman coastal waters at 5 different depths including 5, 10, 20, 50 and 100 m. Sampling was carried out in four seasons of spring, summer, autumn and winter during 2008, 2009 and 2010 on board of R/V Gilan. Altogether, 12 species of zooplankton were identified in 2008, 22 species in 2009 and 14 species in 2010. The zooplankton included four groups: copepoda (4 species), cladocera (8species), rotatoria (10 species) and protozoa (2 species).The increase of diversity in 2009 was due to cladocera and rotatoria groups. The abundance of zooplankton in the spring was 5074 + 7807 ind/m3 more than other season in 2008. The abundance of copepoda in the summer reached the highest value of 3332 ind/m3 and since autumn the abundance gradually decreases and in the winter reached to the lowest value. The most abundance of cladocera was 797 ind/m3 in winter and decreased in summer and autumn. The abundance of rotatoria was 2189 ind/m3 in winter. rotifera and copepoda consisted the main population of Zooplanktons in the winter. The results of 2009 and 2010 showed that the abundance of zooplankton in winter was 2.6 fold of autumn, 1.6 fold of summer and 1.1 fold (1/9 fold in 2010)of spring. After increasing increased of temperature, phytoplankton, and zooplankton in summer, M.leidyi increased too. In the autumn M. leidyi reached to the highest rate and decreased zooplankton. The maximum population of zooplankton was in the layer 0-20 m and in the layer more than 20 meters, the abundance of zooplankton decreased very much. In 216 2008, 2009 and 2010, the abundance of zooplankton was 87, 77 and 77 percent in the layer 0-20 m respectively. In this study, the thermocline was observed in the layer 10 – 20 meters in the spring, that formed a thin layer but in the summer it was in the layer 20 to 50 meters. Temperature decreased between 11 to 15 oC in this layer. The variation of temperature between surfaces to bottom was 10 to 13 oC in spring, 19 to 21 in summer, about 9 oC in autumn and maximum 3 oC in winter. The most biomass of zooplankton was in the west. The biomass of zooplankton in central west and east of Southern of Caspian Sea was 54 %, 22 % and 24 % respectively in 2008, in 2009 was 48%, 33% and 20% respectively and in 2010 was 54 %, 29 % and 16 % respectively .The biomass decreased from west to east. The model of zooplankton designed by principal component analysis (PCA)and linear regression for Southern of Caspian Sea.