The amino acid compositions of 11 Gram–positive and 12 Gram–negative eubacteria were determined from their complete genomes. They were classified into two groups, ‘S–type’ represented by Staphylococcus aureus and ‘E–type’ represented by Escherichia coli, based on their patterns of amino acid compositions determined from the complete genome. These two groups were characterized by their concentrations of Arg, Ala and Lys. Mycoplasmas, which lack a cell wall, belonged to the ‘S–type’, while Gram–positive mycobacteria belonged to the ‘E–type’. Rickettsia prowazekii, Borrelia burgdorferi, Campylobacter jejuni and Helicobacter pylori, which are Gram–negative, belong to the ‘S–type’. The classification into two groups based on their amino acid compositions determined from the complete genome was independent of Gram staining. In addition, the amino acid composition based on the plasmid resembled that based on the parent complete genome.