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The biological soil crusts that appear on the arid soils of Santiniketan, India soon after receiving monsoon rain were studied. The phototrophic organisms in the crusts were principally composed of sheath-forming cyanobacteria belonging to the genera Scytonema and Tolypothrix as the major components along with associated species of 14 different genera. 16S ribosomal RNA (rRNA) sequencing of these organisms showed that they formed a cluster quite different from Leptolyngbya, Microcoleus, and Phormidium, however, were close to Scytonema and Tolypothrix reported from similar biofilms on soils of USA and Costa Rica. All these major cyanobacteria species in soil crust possessed scytonemin in higher proportion than chlorophyll a, suggesting its role in protection from high solar irradiance and UV. Dried crusts started respiring soon after wetting followed by photosynthesis. Nitrogenase activity also revived after 2 to 12 h of wetting and progressed rapidly with longer period of wet conditions coinciding with appearance of heterocysts in the filaments. These results showed that a number of cyanobacteria with distinct sheath layer survived within the soil crusts in desiccated state and revived their metabolic activity soon after receiving monsoon rain thus contributing to carbon as well as nitrogen fixation in the environment and to nutrient mobilization making the soil productive.