Although Buchnera sp. APS, an intracellular symbiont of pea aphids, is a close relative of Escherichia coli, its genome has been extensively modified because of its prolonged intracellular life. In our previous studies on the Buchnera genome, computer analysis predicted three “orphan” genes, yba2, yba3, and yba4, which are open reading frames (ORFs) with no homologs in the database. In this paper, we successfully validated all these orphan genes by RT-PCR and Northern hybridization. The present study also revealed that yba3 and yba4 formed an operon, suggesting that they function in concert. Sequences around transcriptional start sites suggests that these genes are under the control of sigma 70. In view of codon usage and AT bias observed in these genes, it is likely that Buchnera have maintained them for an evolutionarily long time.