Phytoplankton are primarily structured by the water elements, influenced by light intensity, the diversity is different with north and middle of Caspian Sea. It is important to know about diversity, abundance and biomass of phytoplankton in this area, then for this study was done in southern par of Caspian Sea. All samples were taken during 1995-96 and 2006-2007 in 6 transects such as Lisar, Anzali, Sefidroud, Noushahr, Babolsar and Amirabad, respectively. The phytoplankton compositions were changed significantly with seasons (P<0.05). In comparison after Mnemiopsis leidyi arrival, phytoplankton species were increased. Totally 124 species were identified from 2 phylums such as Bacillariophyta and Cyanophyta were 91 and 33 species, respectively. At the present research, the most dominant group was Bacillariophyta and between all species and majority related to Thalassionema nitzchoide specie. Also, during this study, Cyabobacteria community in the Caspian Sea changed in different years and the maximum cell abundance and biomass observed in summer and Shannon-Weaver diversity index changed in this study. During 2006- 2007 (after M. leidyi arrival), the phytoplankton are shown significant changes in diversity at different seasons (P<0.05. The highest amounts of phytoplankton in southern part of Caspian Sea were Cyanophyta and Bacillariophyta phyla, respectively and According to statistical analysis, there was a significant change in seasonal cycle of Cyanophyta concentration. Because decreasing siliconate phytoplankton in the summer, Nodularia spumigena, of Cyanophytes, bloomed in 2005.