Although light and salt stresses are known to enhance the biosynthesis of astaxanthin in certain green algae, the mechanism of their action remains largely unknown. Here we report the regulation of the genes encoding phytoene desaturase (PDS), carotenoid hydroxylase (CHYb), and carotenoid ketolase (BKT) in the green alga Chlorella zofingiensis Dönz under light or sodium chloride (NaCl) stress. High-light illumination (150 μmol photons · m−2 · s−1) up-regulated the transcripts of PDS, CHYb, and BKT and greatly enhanced the biosynthesis of zeaxanthin, canthaxanthin, and astaxanthin. In contrast, sodium chloride stress only up-regulated the transcript of BKT and enhanced the biosynthesis of canthaxanthin and astaxanthin. High-light and NaCl stresses were revealed to result in an increase in the intracellular reactive oxygen species (ROS) level. By applying chemically generated ROS to the algal cells, we determined that 1O2 specifically up-regulated the CHYb gene, whereas •OH up-regulated the PDS and BKT genes. We suggest that high-light and NaCl stresses may stimulate the generation of different ROS, which in turn trigger the up-regulation of specific carotenogenic genes and the enhanced biosynthesis of carotenoids in C. zofingiensis.