Degradation and recycling of intracellular components via autophagy is conserved among eukaryotes. This catabolic process is mediated by autophagy-related (ATG) proteins, which have been identified in different systems including yeasts, mammals and plants. The genome of the model alga Chlamydomonas reinhardtii contains homologues to yeast and plant ATG genes although autophagy has not been previously described in this organism. In our study, we report the molecular characterization of autophagy in Chlamydomonas. Using the ATG8 protein from Chlamydomonas as a molecular autophagy marker, we demonstrate that this degradative process is induced in stationary cells or under different stresses such as nutrient limitation, oxidative stress or the accumulation of misfolded proteins in the endoplasmic reticulum. Our results also indicate that TOR, a major regulator of autophagy, inhibits this process in Chlamydomonas.