Display omitted •Nutrients and salinity influence the carotenoid composition in microalgae.•Maximum carotenoid content in Synechocystis sp. CCNM 2501 is 7.99mgg−1 DW.•>4 folds higher echinenone in Zarrouk’s media as compared to BG11 and Chu’s 10.•>3 folds higher β-carotene in 1M salinity compared with non saline medium. Nutrients are the deciding factors in the biological production of bioactive compounds. Various growth media like BG11, Zarrouk’s and Chu’s 10 were studied for carotenoid production in Synechocystis sp. CCNM 2501. Maximum carotenoid content (dry weight basis) was found in Zarrouk’s medium (ZM, 7.99mgg−1) followed by BG11 (5.13mgg−1). Echinenone content was 4 times higher in ZM (3.81mgg−1) as compared to BG11 (0.95mgg−1) and Chu’s 10 (0.77mgg−1). Being an economical medium, BG11 was selected for carotenoid production. Further, increase in salinity from 0 to 0.2M in BG11 medium increases total carotenoid content from 5.82 to 7.05mgg−1 and later it declines to 6.23mgg−1 (1M). 3 times more β-carotene is produced at 1M salinity as compared to control BG11. The variation in carotenoid composition with change in nutrients/salinity can be a good strategy to enhance certain targeted carotenoids.