The cosmopolitan terrestrial cyanobacterium Nostoc commune is considered to be a prokaryotic model anhydrobiote which can tolerate the simultaneous stresses of desiccation, UV irradiation, and oxidation. The mechanisms behind the tolerance are thought to involve multiple processes, and the ability to produce the UV sunscreen including mycosporine-like amino acids (MAAs) and scytonemin appears to be a required factor. In this study, we examined three genotypes of N. commune colonies. These genotypes showed different water extract UV-absorption spectra and structurally distinct MAAs were found in each genotype; whereas, no difference was found in terms of the ethanol extracts of these genotypes; producing the same 544-Da scytonemin. These compounds had potent radical scavenging activities in vitro and the results confirmed that they have multiple roles as the UV protectant and antioxidant relevant to anhydrobiosis in N. commune. These genotypes of N. commune exclusively produced their own characteristic MAAs, which supports that MAA composition could be a chemotaxonomic marker for the classification of N. commune. According to the amounts, structures and fragmentation patterns of the MAAs, different MAA biosynthetic pathways are predicted in each genotypes. Further molecular genetic studies are required to identify the enzymes and associated genes in the predicted biosynthetic pathway.