Buchnera aphidicola is a prokaryotic endosymbiont of the aphid Schizaphis graminum. With the polymerase chain reaction (PCR) and oligonucleotide primers to conserved regions, two DNA fragments of the endosymbiont alpha-operon and L20 operon were amplified, cloned into Escherichia coli, and their sequences were determined. The results indicated that the organization of the endosymbiont genes on these fragments was identical with that of the corresponding operons of E. coli. The 1032 base pair (bp) fragment of the alpha-operon contained the genes for small ribosomal subunit proteins S11 and S4, followed by the gene for the alpha-subunit of RNA polymerase (alpha-RNAP). The 702-bp fragment of the L20-operon contained the genes for initiation factor-3 (IF3) and large ribosomal subunit proteins L35 and L20. As in other prokaryotes, the genes of the alpha-operon and the L20-operon were present as single copies in the genome of B. aphidicola. Comparisons of the amino acid sequences of these proteins were consistent with the previously established close relationship between B. aphidicola and E. coli and a distant relationship to species of Bacillus.