A feature of the mitochondrial electron transport chain in plants, some protists and many fungi is the presence of two terminal oxidases, the energy-conserving cytochrome oxidase and another termed alternative oxidase (AOX). AOX branches from the main respiratory chain, directly coupling the oxidation of ubiquinol with reduction of oxygen to water. The AOX genes can be divided into two discrete subfamilies, AOX1 and AOX2. Although AOX has been proposed to play essential roles in stress tolerance of organisms, the role of subfamily AOX2 is largely unknown. In the model green alga Chlamydomonas reinhardtii, two genes have been identified that encode for AOX, AOX1 and AOX2. To test AOX2 transcriptional regulation in this alga, we used a real-time PCR analysis and an artificial microRNA approach. The C. reinhardtii AOX2 gene is up-regulated by oxygen or copper deprivation. Moreover, in dark-adapted unstressed cells, AOX2 is induced. Together, our results imply that the AOX2 gene is a stress-inducible and is regulated by the copper response regulator 1 (CRR1), probably together with yet-unknown regulatory factor(s).