During the last decade, scytonemin and mycosporine-like amino acids (MAAs) have gained considerable attention as an efficient natural photoprotectants against damaging ultraviolet (UV) radiation. In the present investigation biological crusts from different natural habitats such as roof top, bark of Mangifera indica, usar land, window ledge and agriculture field were examined for the presence of photoprotective compounds such as scytonemin and MAAs. These habitats represent diverse environments having high solar irradiance, high temperature, desiccation and nutrient depleted conditions. Biological crusts primarily composed of cyanobacteria such as Scytonema sp., Lyngbya sp. and Nostoc sp. Chlorophyll, carotenoids, scytonemin and MAAs were analyzed using absorption spectroscopic analysis. Identification and partial purification of scytonemin and MAAs were done by HPLC analysis which revealed the presence of scytonemin and MAAs in all the samples. Scytonemin had a retention time ranging from 1.43-3.85 min with absorbance maxima at 252, 278 and 386 nm and peaks of MAAs had a retention time ranging from 1.99-7.19 min with corresponding absorbance maxima at 309, 310, 330 and 332 nm corresponding to mycosporine-taurine, mycosporine-glycine, asterina-330 and palythinol respectively. Based on these findings, we conclude that photoprotective compounds such as scytonemin and MAAs may play a vital role not only in photoprotection but also in the survival and sustainability of cyanobacterial life, which are dominant organisms of most of biological crusts samples, in adverse environmental conditions such as under high solar irradiances, temperature, desiccation and nutrient depletion.