Due to the increasing demand for fish and limited fish stocks, caused to aquaculture as an important way to meet protein needs of a growing world population and pressure to reduce fishing effort from the Sea, and increasing the income of the coast, especially in low-income countries should be considered. In this study population structure of phytoplankton in shrimp vannamei (PL12) were evaluated with brackish water of the Caspian Sea. For cultivation of brackish water (ppt 43/0 ± 52/10) was funded from the Caspian Sea. Experiments on 13 concrete circular pool with a sandy bed (with an area of 78 square meters) in 5 treatments and 3 replications for each treatment. Breeding period is 75 days. In this study identified 20 genera of phytoplankton from five division of the Phytoplankton. Phylum Cyanophyta, with 30 percent of the identified genera that much more constituted. And the phylum Chlorophyta with 25 percent, of Bacillariophyta 20 percent Pyrrophyta 20 percent and Euglenophyta 5 percent had the lowest frequency. Chlorophyta with 25 percent allocated to the division, with 20 percent of Bacillariophyta, with 20 percent of the division; Pyrrophyta Euglenophyta division with 5 percent had the lowest frequency. Euglenophyta phylum was identified as a species. Genus Chlorella green algae Chlorophyta phylum in all the pools had been sampling at various times. But some genus of the different stages of sampling there has been only once. Genus Chaetoceros of Bacillariophyta and genus Chlamidomunas of Chlorophyta in different more stages were of sampling. In this study, cell abundance and treatment time of was varies.The maximum cell abundance of phytoplankton in September and lowest cell abundance in July. The micro-algae cell growths were almost equal at a time. In July, August and September, to the greatest concentration of phytoplankton belongs to Chlorophyta43/8 ± 13/5, 56/7 ± 18/5 and 603/3 ± 170/2 (cells per liter × 106 ), respectively, and in group 2, group 1 have been affected by the genus Chlorella.