The study of community composition of algae is essential for understanding the structure and dynamics of the aquatic ecosystem and for evaluating the eutrophic level of the water body. A high-performance liquid chromatographic (HPLC) method based on a reversephase C 18 nonpolar column was developed for the main algal taxa, which includes cyanophytes, bacillariophytes, euglenophytes, dinophytes, and chlorophytes. Based on the elution order using HPLC, 19 pigments were identified, and they were chlorophyllide a, 19′-butanoyloxyfucoxanthin, chlorophyll c 1 + c 2 , phephorbides a, peridinin, methyl-chlorophyllide a, fucoxanthin, neoxanthin, violaxanthin, myxoxanthophyll, diadinoxanthin, diatoxanthin, lutein, zeaxanthin, chlorophyll b allomer, chlorophyll b, chlorophyll a allomer, chlorophyll a, and β,β-carotene. A comparison study of cell microscopic counts and accessory pigment analysis indicated that HPLC analysis could be a useful tool for monitoring phytoplankton communities and their abundance.