Autophagy is a self-degradation system wherein cellular materials are recycled. Although autophagy has been extensively studied in yeast and mammalian systems, integrated stress responses in microalgae remain poorly understood. Accordingly, we carried out a comparative study on the oxidative stress responses of Chlamydomonas reinhardtii wild-type and a starchless (sta6) mutant previously shown to accumulate high lipid content under adverse conditions. To our surprise, the sta6 mutant exhibited significantly higher levels of lipid peroxidation in the same growth conditions compared to controls. The sta6 mutant was more sensitive to oxidative stress induced by H2O2, whereas the wild-type was relatively more resistant. In addition, significantly up-regulated autophagy-related factors including ATG1, ATG101, and ATG8 were maintained in the sta6 mutant regardless of nitrogen availability. Also, the sta6 mutant exhibited relatively higher ATG8 protein level compared to wild-type under non-stress condition, and quickly reached a saturation point of autophagy when H2O2 was applied. Our results indicate that, in addition to the impact of carbon allocation, the increased lipid phenotype of the sta6 mutant may result from alterations in the cellular oxidative state, which in turn activates autophagy to clean up oxidatively damaged components and fuel lipid production.