The present study is focused on protein degradation during astaxanthin synthesis in Haematococcus pluvialis under high irradiance and nitrogen deficient conditions. It was found that with the onset of astaxanthin synthesis in the cultures of high light and nitrogen-free (HF), high light and nitrogen-repletion (HR), and low light and nitrogen-free (LF), (1) endopeptidase (EP) activities increased along with decrease in protein content, (2) asparagine in HF and HR rose significantly before the first 4 and 5 day, but fell after that time. While, it increased slowly and continuously in LF, (3) ammonium increased continuously in HF and HR, whereas in LF, it was detected on the sixth day, and increased slowly on the following days. By contrast, in low light and nitrogen-repletion culture, (LR), the contents of protein and asparagine as well as EP activity were maintained relatively constant, no astaxanthin and ammonium were detected. Furthermore, when HF was sealed and bubbled with CO2-free gas (O-2 and N-2) astaxanthin content increased as the protein level decreased. These results strongly suggest that (1) the degraded protein served as a substitutive carbon source, to some extent, for the biosynthesis of astaxanthin, (2) endopeptidase was involved in the degradative process, (3) for detoxification, part of the ammonium generated by protein degradation was transiently stored in asparagine, whereas the rest of it was expelled into the culture broth.