Abstract: Pigments in seston of Lake Donghu and enclosures were studied by means of HPLC. There were totally 20 pigments separated in the study and the major carotenoids were fucoxanthin, alloxanthin, lutein, and zeaxanthin. The annual average concentration of each pigment at Station Ⅰ was always the highest, and Station Ⅱ ranked the second. Chlorophyllide a was the major degradation product of Chl a, comprising about 5% of the Chl a concentration. Other Chl a derivatives appeared mostly in minor quantities. The results of the enclosure experiment showed that there was a significant correlation between the concentration of the marker pigment and the biomass of the correspondent algae group. The correlation coefficients between Chl a and total phytoplankton biomass, Chl b and green algae, alloxanthin and cryptophytes, fucoxanthin and diatoms were 0.84,0.77,0.83and 0.68,respectively. The results suggest that pigment analysis is a useful tool for monitoring phytoplankton structure because it is rapid and time saving.