Ability to produce UV-absorbing compounds by terrestrial cyanobacterium Nostoc commune is thought to be a required factor in tolerance to UV radiation. Mycosporine-like amino acids (MAAs) and scytonemin are well known UV-absorbing compounds in cyanobacteria that partially or completely avoid the harmful effects of long term UV radiation exposure. In this study, three genotypes of N. commune colonies were collected, although no obvious differences in their appearance could be observed by eye. The MAA and scytonemin content of these genotypes were identified from water and ethanol extract of N. commune, respectively. These results show that the elution profiles of the pigments from water extracts of these three genotypes of N. commune exclusively produced their own characteristic MAAs; the first genotype expresses a 478-Da MAA as a main MAA, the second genotype expresses a 1,050-Da MAA as a main MAA, and the third genotype expresses a 612-Da MAA as a main MAA. No difference was found in terms of the elution profiles of the pigments from ethanol extracts of these three genotypes; producing the same 544-Da scytonemin. These purified MAAs and scytonemin had radical scavenging activities in vitro; the 1,050-Da and 612-Da MAAs were the main water-soluble radical scavengers in the water extract, as they provided approximately 27% and 20% of the water-soluble radical scavenging activities in their colonies, respectively, and the scytonemin-associated activity accounted for approximately 10% of the total recovered activity. These results suggest that these MAAs and scytonemin have multiple roles as a UV protectant and an antioxidant relevant to anhydrobiosis in N. commune.