Various cyanobacterial (Microcystis aeruginosa, Anabaena sp., Merismopedia sp., Aulosira fertilissima, Oscillatoria sp. and Gloeocapsa sp.) and algal samples were collected from four historical Kunds of Varanasi, India, and were investigated for the presence of photoprotective and pharmaceutically important compound such as mycosporine-like amino acids (MAAs). High-performance liquid chromatography (HPLC) and UV-Vis spectrophotometry analyses reveal the presence of five different MAAs, identified as porphyra-334 (λmax=334 nm), palythine (λmax=320 nm), palythenic acid (λmax=337 nm), mycosporine-glycine (λmax=310 nm) and mycosporine-methylamine-serine (λmax=327 nm) having retention times (RT) of 3.62, 1.65, 4.15, 2.55 and 1.51 min respectively. These MAAs were further characterised by using Fourier Transform Infrared (FTIR) analysis. To the best of our knowledge this is the first report of its kind from different historical Kunds of Varanasi. Photoprotective MAAs may help cyanobacteria and other algal assemblage to protect themselves from deleterious radiations and in turn to colonize the historical Kunds. These MAAs containing organisms could be a valuable source of photoprotective compounds of pharmaceutical importance in developing natural sunscreens.