AbstractCyanobacteria are cosmopolitan in distribution, forming a prominent component of microbial populations in both aquatic as well as terrestrial ecosystems. They are the dominant microflora in rice‐fields, where they significantly contribute to fertility as a natural biofertilizer. The fluence rates of UV‐B radiation impinging on the natural habitats is of major concern since being photoautotrophic organisms, cyanobacteria depend on solar radiation as the primary source of energy. UV‐B radiation causes reduction in growth, survival, pigment and protein content, heterocyst frequency and fixation of carbon and nitrogen in cyanobacteria. However, a number of cyanobacteria synthesize water soluble colorless mycosporine‐like amino acids (MAAs) and the lipid soluble yellow‐brown colored sheath pigment, scytonemin to counteract the damaging effects of UV‐B. Anabaena sp., Nostoc commune, Scytonema sp. and Lyngbya sp. were isolated from rice‐fields in India and screened for the presence of photoprotective compounds. Spectroscopic and biochemical analyses revealed the presence of shinorine, a bisubstituted MAA containing both glycine and serine group with an absorption maximum at 334 nm in all cyanobacteria except Lyngbya sp. There was a circadian induction in the synthesis of this compound by UV‐B. Polychromatic action spectra for the induction of MAAs in Anabaena sp. and N. commune show the induction to be UV‐B dependent peaking at 290 nm. Another photoprotective compound, scytonemin, with an absorption maximum at 386 nm (also absorbs significantly at 300, 278, 252 and 212 nm) was detected in all cyanobacteria except Anabaena sp. In addition, two unidentified, water‐soluble, yellowish and brownish compounds with an absorption maximum at 315 nm were recorded only in Scytonema sp. The spectral characteristics of these compounds neither matches with MAAs nor with scytonemin and seems to be a novel compound acting as an effective UV screens. In conclusion, a particular cyanobacterium having photoprotective compounds may be a potent candidate as biofertilizers for crop plants.