Amirkelayeh lagoon is situated in 50o 10' -50o 12' 30" E and 37o 19' 30" - 37o 22' 30" N. The lagoon covers an area of 1230 hectars, is protected by Department of the Environment in 1970. The vegetation of Amirkelayeh lagoon was studied, using the Braun-Blanquet school (Zygmatist). Based on the analysis of phytosociological data by Factorial Correspondence Analysis and Hierarchical Ascendent Classification methods IS associations were recognized They belong to 3 classes, 3 orders and 7 alliances. The following associations constitute the major part of the natural vegetation of the area: Phragmitetum australis, Potametum pectinati, Cladietum marisci, Ceratophylletum demersi, Nitelletum sp. The distribution of plant associations are affected by physical and chemical properties of water (e.g. density of salts and contaminants, clearness, temperature, pH, EC, DO, COD, BoD), depth and intensity of water, quality and quantity of sediments and biological factors. Vegetation map of Amirkelayeh lagoon is prepared in 1: 25000 scale based on phytosociological data by using combination of symbols and colors.