Aquatic photosynthetic organisms, including the green alga, Chlamydomonas reinhardtii, induce a set of genes for a carbon concentrating mechanism (CCM) through the CO2-signalling system, to acclimate to CO2-limiting stress conditions. We have described a regulatory gene, Ccml, which was shown to regulate CCM induction in C. reiuhardtii. In this review, we summarize the current understanding of the regulatory process, which controls the expression of genes for the CCM. In particular, CCM1-regulated genes and possible functions of Ccml in the CO2-signalling pathway are discussed, in relation to findings in other green algae and cyanobacteria.