A novel index,Normalized Difference Chlorophyll Index (NDCI),is introduced in this study to estimate the chlorophyll-a (Chl.a) concentration from Hyperspectral Hyperion data,HSI data,and measured Chl.a concentration data for Lake Taihu and Lake Chaohu in eastern China.The best bands were selected by analyzing spectral channels of the Hyperspectral data and the spectral characteristics of the water.The Chl.a concentration was estimated by considering the regression relationships between NDCI and the measured Chl.a concentrations through the analysis of the NDCI reflection factor and points data of measured samples.Comparing the results of the NDCI method to that of the normal ratio,first-order differential,and three bands methods, the NDCI method has performed better in simplicity,accuracy and applicability than the other three methods in the estimation of Chl.a concentration in case Ⅱ waters.