Phycocyanin, a functional protein found in blue-green algae, with characteristic absorption peak around 620 nm, can be used to detect the quantity of blue-green algae in waters. Spectral characteristics of phycocyanin were studied by measuring hyperspectral water leaving radiance and absorption curve, and the results showed that the absorption peak of phycocyanin around 620 nm was evident in the curve of water leaving radiance. Bio-optical model of phycocyanin was set up with analytical methods and calibrated with error analysis. Linear relationship between phycocyanin concentration measured and that retrieved with calibrated bio-optical model (R = 0.755) was better than that retrieved with the band ratio of 709 nm/620 nm (R = 0.729), which proved that the calibration was necessary for improving the accuracy of phycocyanin concentration.Keywords: phycocyanin, case II waters, hyperspectral remote sensing model, calibrated algorithm.Phycocyanin, generally existing in blue-green algae, can be used as index for detecting blue-green algae, for the characteristic absorption peak and fluorescence. In the process of growth and decay, blue-green algae will produce toxin into water environment, which seriously deteriorated water quality. Real time detection of blue-green algae was very important for knowledge of the distribution and control of blue-green algal bloom.In case II waters, it was very difficult to retrieve single pigment concentration, the high concentration of suspended solids and CDOM. In early 1990s, after studying the concentration of chlorophyll a in inland water with hyperspectral remote sensing, Gitelson [1] used the ratio of red and infrared to retrieve the concentration of chlorophyll a and obtained good results. Gons [2,3] further studied the ratio of upwelling irradiance to downwelling irradiance just under water at 675 nm and 702 nm and backscattering at 778 nm to calculate chlorophyll a in Lake Taihu and Lake Chaohu and obtained better result. Based on the analytical algorithm of chlorophyll a in case I waters by Gordon [4] and Morel [5] , Lee Z P [6] developed the optical remote sensing model of chlorophyll a in case II waters. These studies successfully avoided the effect of suspended solids and CDOM, and provided the direction to retrieve the phycocyanin concentration in waters with hyperspectral remote sensing.In recent years, some researchers have preliminary studied the bio-optical model of phycocyanin in waters. Wheeler [7] monitored the distribution of blue-green algae in Lake Champlain and Lake Vermont with Landsat TM, calibrated with the data of Flow CytoMeter, and obtained good results. Vincent [8] detected phycocyanin with Landsat TM in Lake Erie, regressed with fluorescence ratio of phycocyanin and chlorophyll a, and the correlation coefficient can reach 0.77. After studying the distribution of phycocyanin in inland water with high concentration of suspended solids and CDOM, Simis [9] set up the bio-optical model of phycocyanin by retrieving the phycocyanin absorption at 6...