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There are many serious problems causing a food crisis such as desertification, population explosion, and environmental destruction, suggesting that a severe food crisis will become reality across the globe. Therefore, the transgenic plants, which have tolerance to environmental stresses, may take on greater and greater importance in attempts to increase food production. Aquatic photosynthetic organisms, such as prokaryotic cyanobacteria and eukaryotic green algae, are considered as an evolutionary origin of higher plants and their basic metabolisms including photosynthesis are similar to higher plants. Thereby, stress responsive genes or reactions from these organisms may be exceedingly advantageous sources for creation of stress-tolerant transgenic plants. In this study, the physiological roles and biosynthesis of abscisic acid (ABA), well known as a signal molecule in the adaptation to environmental stresses, in microalgae were investigated from the point of the view of its functional evolution in the response to environmental stresses. Chlamydomonas reinhardtii, a green alga, and Synechocystis sp. PCC 6803, a cyanobacterium, were employed in this study as model organisms. It is expected that this comparative analysis will provide basic information for the creation of stress-tolerant transgenic plants. ABA may act in C. reinhardtii as a signal molecule to induce antioxidant reactions for elimination of reactive oxygen species, but not to induce specific response reactions to mitigate water stresses. In Synechocystis, on the other hand, exogenously added ABA did not influence the growth and gene expression. Moreover, ABA did not relieve growth suppression caused by water and oxidative stresses. From the carotenoid composition and bioinformatic analysis, it can be suggested that the ABA biosynthetic pathway generally found in higher plants exists completely in C. reinhardtii, but incompletely in Synechocystis.