Chlorophyll a (chl a) has been used as an indicator for phytoplankton biomass in pelagic ecosystems due to the relative ease of measurement and selectivity for autotrophs in mixed plankton assemblages. However, the use of chl a as an indicator for phytoplankton biomass is restricted due to its inability to resolve taxonomic differences of phytoplankton and the highly variable relationship of chl a with phytoplankton. Here, we describe the analysis of High-Performance Liquid Chromatography (HPLC) photosynthetic pigment data using CHEMTAX, which is a matrix factorization program that uses chemical taxonomic indices (phytoplankton carotenoids) to quantify the abundance of phytoplankton groups. Compared to direct microscopic counting that can distinguish species within broad groups, the resolution of taxonomic groups by CHEMTAX is generally coarse. It can only distinguish between diatoms, dinoflagellates, cryptophytes, cyanobacteria, chlorophytes, prasinophytes, and haptophytes. However, CHEMTAX analysis is much faster and less expensive than microscopic counting methods. HPLC pigment observations were taken in the spring, summer, fall, and winter in 2005～2006 within Gamak Bay, South Korea. CHEMTAX results revealed that diatoms were the dominant taxonomic group in Gamak Bay. In inner Gamak Bay, the ratio between diatoms and cryptophytes was 75～80%, and the ratio between dinoflagellates and cryptophytes was 10～15%. In outer Gamak Bay, the ratio between diatoms and cryptophytes was 85～90%, and the ratio between dinflagellates and cryptophytes was only 1～5%. The population structure was seasonal. Relative diatom populations were less in the summer than the winter season.