This study focuses on spatial and temporal distribution and species composition of phytoplankton in the south-western Caspian Sea between July 2009 and March 2010. Samples were collected from 11 stations along three transects: Lisar, Anzali and Sefidrood. Among 44 identified phytoplankton species, diatoms (70.2%) and cyanophytes (25.0%) were dominant. The average phytoplankton abundance was calculated as 1.085E + 05 cells l−1. Among the phytoplankton groups, diatom density was higher (70.2%) than two out of three of total abundance in density of 1.085E + 05 cells l−1. Cyanophytes were the second important group (25.0%) contributing to total phytoplankton. Dinoflagellates, chlorophytes and euglenoids were other contributors to total phytoplankton. Diatoms Dactyliosolen fragilissimus and Skeletonema costatum and cyanophyte Oscillatoria sp. numerically dominated in the system. There were major changes in phytoplankton composition and average phytoplankton density was higher than those documented in 1996–1997 and 2005. The average concentrations of dissolved inorganic nitrogen (DIN), dissolved inorganic phosphorus (DIP) and dissolved inorganic silicate were 14.5 ± 6.32, 1.14 ± 0.44 and 5.10 ± 3.98 μM, respectively, and these concentrations were strikingly high. Increases in DIN and DIP concentrations were more than twofold compared to recorded values during the last 2 decades due to the eutrophication. Fluctuations in nutrients played an important role in the variation of phytoplankton composition and abundance. Chlorophyll-a concentrations varied between 3.22 and 16.1 μg l−1 and there was a significant increase in chlorophyll-a (8.13 ± 5.72 μg l−1) compared to the values in 1996–1997 (1.44 ± 1.48 μg l−1), 2001 (2.62 ± 1.48 μg l−1) and 2005 (2.14 ±1.94 μg l−1).