Aims Green algae (Chlorophyta), as a diverse group of algae, has almost omnipresent distribution in the Caspian Sea and plays an important role in ecosystem functioning. The aim of this study was to investigate the spatial and temporal distribution and biomass trend of planktonic green microalgae (Chlorophyta) in southeast of the Caspian Sea. Materials & Methods This experimental study was performed by sampling water from south of the Caspian Sea in Mazandaran province during the winter 2015 and summer 2016. Water sampling was done along two half-lines perpendicular to the estuaries of “Tajan” and “Babolrood” rivers in 8 stations and 4 depths (less than 1, 5, 10, and 20 m) in the euphotic zone, at 8 stations along the linear transects. Settlement method was applied to the preserved samples in formaldehyde 4%, in order to the qualitative and quantitative analysis of phytoplankton. The biomass of Chlorophyta was calculated, using the geometric shape method. The data were statistically analyzed, using PRIMER 6 and SPSS 19 software and the diagrams were drawn by Excel 2013. Findings Of total 29 identified Chlorophyta species, 28 species were present in the summer with the highest abundance of Chlorella sp. (1395×105±671×104 N/m3) and, 19 species were observed during the winter, with the highest abundance of Binuclearia sp. (456×105±155×104 N/m3). Binuclearia sp. also showed the highest biomass in both seasons. Conclusion The diversity of Chlorophyta is influenced by seasonal variations. Estuaries are the richest stations in terms of abundance and biomass of planktonic Chlorophyta in summer.