When whole-cell extracts are analyzed, proton nuclear magnetic resonance $(^1H;NMR)$ spectroscopy provides biochemical profiles that contain overlapping signals of the majority of the compounds. To determine whether cyanobacteria could be taxonomically discriminated on the basis of metabolic fingerprinting, we subjected whole-cell extracts of the cyanobacteria to $^1H;NMR$. The $^1H;NMR$ spectra revealed a predominance of signals in the aliphatic region. Principal component analysis (PCA) of the data then enabled discrimination- of the cyanobacteria. The hierarchical dendrogram, based on PCA of the aliphatic region data, showed that six cyanobacterial taxa were discriminated from two eukaryotic microalgal species, and that the six taxa could be subsequently divided into three groups. This agrees with the current taxonomy of cyanobacteria. Therefore, our overall results indicate that metabolic fingerprinting using $^1H;NMR$ spectra and multivariate statistical analysis provide a simple, rapid method for the taxonomical discrimination of cyanobacteria