Aquatic photosynthetic organisms can acclimate to the variable and limiting availability of CO(2) by operation of carbon-concentrating mechanism (CCM) that allows them to optimize carbon acquisition for photosynthesis. The CCMs of both eukaryotic alga and cyanobacteria function to facilitate CO(2) assimilation, when inorganic carbon (Ci; CO(2) and/or HCO(3)(-)) is limited. By active Ci uptake systems, internal Ci levels are increased and then carbonic anhydrase supplies sufficient CO(2) to ribulose 1,5-bisphosphate carboxylase/oxygenase by the dehydration of accumulated bicarbonate. Although the molecular components of CCM have been intensively studied in cyanobacteria, significant advances in understanding of the eukaryotic CCM have been achieved especially in a model green alga, Chlamydomonas reinhardtii. Recent accumulation of genomic sequence data of algae leads to start comparative genomic analyses of functional components of eukaryotic CCM. This review focuses on the recent advances in identifying and characterizing the components of the CCM by transcriptome analyses of the Chlamydomonas cells that are transferred to CO(2)-limiting stress conditions in light.