Two kinds of Haematococcus pluvialis cells (green vegetative cells cultivated under optimal cell culture conditions and red cyst cells maintained under high light stress conditions to induce astaxanthin production) were used to investigate the protein expression profiles by two-dimensional electrophoresis, image analysis, and peptide mass fingerprinting. The cellular accumulation of astaxanthin was evident after exposure to high light intensity and reached the maximum cellular level after 78 h of high light stress. In a 2-D electrophoresis analysis, 22 proteins were upregulated over 2-fold in the red cyst cells when compared with the green vegetative cells and selected for further analysis by chemically assisted fragmentation (CAF)-MALDI-TOF sequencing to identify the protein functions. Among 22 different spots, several key enzymes specific to the carotenoid pathway, including isopentenyl pyrophosphate isomerase (IPP) and lycopene $eta$-cyclase, appeared in H. pluvialis after exposure to high light intensity. Therefore, IPP and lycopene $eta$-cyclase would appear to be involved with carotenoid accumulation in the cytoplasm, as these peptides were preferentially upregulated by high light intensity preceding an increase in carotenoid, and only these forms were detected in the red cyst cells.