Blue green algae are known to form algal blooms in many parts of the world. Microcystis sp is colony forming bloom seen in hypersaline lake Tsokar in Ladakh. The lake was studied for three years from 2011-2013 and sampling of phytoplankton and water sample for various parameters was carried out in early summer and late summer season. Nutrient enrichment with high phosphate content with presence of Microcystis aeruginosa bloom was seen in late summer in the lake. The formation of algal bloom in late summer each year dominated phytoplankton with decreased diatom density in the lake. The high salinity, nutrient enrichment in the lake and presence of Microcystis bloom may affect ecology of the lake in the future. The nutrient enrichment needs to be reduced for reducing algal blooms and keeping the lake healthy.