The Chlorophyll-a (Chla) concentration in Bosten Lake was estimated and mapped using the data of the Medium Resolution Imaging Spectrometer (MERIS) on board the ENVIronmental SATellite (ENVISAT) platform. The fixed aerosol option was chosen and local aerosol optical thickness was used in SeaDAS. The Chla concentration was retrieved by the OC3E algorithm and verified by Field data with high correlation coefficient of 0.79. It showed strong horizontal heterogeneities, which is high at the Huangshuigou region, mediate along the boundary area, and low at the middle of the lake, and decreases from the boundary to the center of the Lake. Its spatial distribution is controlled by the location of inlet and outlet and the type and quantity of discharging around the lake. On sep. 22, 2010, its value is up to 10.98 mg m-3. The minimum, maximum, average and median value of Chla concentration on Aug. 6, 2011 from MERIS data in Bosten Lake is 2.72, 8.93, 3.90 and 3.69 mg m-3.