Mycosporine-like amino acids (MAAs) are UV-absorbing pigments, and structurally unique glycosylated MAAs are found in the terrestrial cyanobacterium Nostoc commune. In this study, we examined two genotypes of N. commune colonies with different water extract UV-absorption spectra. We found structurally distinct MAAs in each genotype. The water extract from genotype A showed a UV-absorbing spectrum with an absorption maximum at 335 nm. The extract contained the following compounds: 7-O-(b-arabinopyranosyl)- porphyra-334 (478 Da), pentose-bound shinorine (464 Da), hexose-bound porphyra-334 (508 Da) and porphyra-334 (346 Da). The water extract from genotype B showed a characteristic UVabsorbing spectrum with double absorption maxima at 312 and 340 nm. The extract contained hybrid MAAs (1050 Da and 880 Da) with two distinct chromophores of 3-aminocyclohexen-1-one and 1,3-diaminocyclohexen linked to 2-O-(b-xylopyranosyl)-b-galactopyranoside. A novel 273-Da MAA with an absorption maximum at 310 nm was also identified in genotype B. The MAA consisted of a 3-aminocyclohexen- 1-one linked to a c-aminobutyric acid chain. These MAAs had potent radical scavenging activities in vitro and the results confirmed that the MAAs have multiple roles as a UV protectant and an antioxidant relevant to anhydrobiosis in N. commune. The two genotypes of N. commune exclusively produced their own characteristic glycosylated MAAs, which supports that MAA composition could be a chemotaxonomic marker for the classification of N. commune.