A computer search for gene arrangements that are present in Gram-positive bacteria but are absent from Proteobacteria and vice versa was carried out. Four such arrangements were detected, based on which major bacterial phyla were divided into two groups; Thermotoga, Deinococcus-Thermus, Chloroflexi (green non-sulfur bacteria), and Fusobacteria, represent Gram-positive bacterial gene arrangements, while Aquifex, Spirochetes, Planctomycetes, Chlorobi (green sulfur bacteria), Bacteroides show Proteobacterial arrangements. The division is almost consistent with another partition of the major phyla based on the comparison of domain architectures of RNA polymerase subunits and sigma factor, suggesting a fundamental split of the major bacterial phyla at an early stage of bacterial evolution.