Growth, morphological variation, and liquid chromatography-photodiode array detection-mass spectrometric analysis of pigments have been studied in a diazotrophic cyanobacterium Anabaena cylindrica in response to NaCl stress. The chlorophyll and cellular protein contents increased initially in response to 50 mM NaCl. Further increment in NaCl concentration, however, resulted in a significant decrease in both chlorophyll and cellular protein. A. cylindrica cells subjected to NaCl stress also showed morphological variations by having alteration in their size and volume. A. cylindrica cells subjected to NaCl stress also exhibited altered plastoquinone and chlorophyll-a (chl a) levels in comparison to its NaCl-untreated counterpart. Furthermore, a relative increase in plastoquinone level and a subsequent decrease in chl a level were recorded in NaCl adapted cells of A. cylindrica in response to NaCl stress. These results suggest that owing to adaptation various morphological, physiological, and biochemical changes occur in the cyanobacterium A. cylindrica in response to NaCl stress.