In this research, Calothrix sp. ISC 65 was characterized physiologically by the combination of extremely low irradiance (2 μEm -2 s -1 ), different alkalinity (pH 7, 9, 11), and extremely limited carbon dioxide concentration (no aeration, no carbon dioxide enrichment).Spectroscopical analysis showed that pH 9, after 96 hours, caused a significant increase in growth rate, chlorophyll, and phycocyanin production. A lower (pH of 7) caused a decrease of phycobilisome production even after 24 hours. Excitation of the light harvesting complex and the reaction center of photosystems resulted from a pH of 9. Phycocyanin seems to be the main part of phycobilisome but pH 9 caused phycoerythrin and allophycocyanin production excitation in the outer part of the photosynthetic antenna as well. A fluorimetric and photosynthesis-irradiance curve analysis showed that increasing alkalinity (up to pH 9) caused an increase in photosynthesis efficiency and a decrease of non-photochemical fluorescence especially after 96 hours. PSII : PSI ratio increased by increasing alkalinity from pH 7 to 9 and reached the highest level after 96 hours. Surface response plot analysis showed that there is a narrow border line around pH 9 and 96 hours which caused the highest PSII : PSI ratio. FTIR analysis showed that alkalinity caused configuration changes of the functional groups. The difference of the functional group patterns between pH 7 and 11 was significant especially after 24 hours. Differences in asymmetric carbon vibration, lipid stretching and OH bending of the polysaccharides occurred with both pH 9 and 11 treatments. pH 9 caused the most physiological activities in Calothrix sp. ISC 65 at extremely limited irradiance and carbon dioxide concentration. K e y w o r d s : alkalinity, Calothrix, cyanobacteria, dissolved inorganic carbon, limited irradiance A b b r e v i a t i o n s : APC  allophycocyanin, CCM  carbon dioxide concentrating mechanism, DIC  dissolved inorganic carbon, PBS  phycobilisome, PC  phycocyanin, PE  phycoerythrin, PSI, PSII  photosystems I and II