Almost all aphid species (Homoptera, Insecta) have 60–80 huge cells called bacteriocytes, within which are round-shaped bacteria that are designated Buchnera1. These bacteria are maternally transmitted to eggs and embryos through host generations, and the mutualism between the host and the bacteria is so obligate that neither can reproduce independently2. Buchnera is a close relative of Escherichia coli3, but it contains more than 100 genomic copies per cell4, and its genome size is only a seventh of that of E. coli5. Here we report the complete genome sequence of Buchnera sp. strain APS, which is composed of one 640,681-base-pair chromosome and two small plasmids. There are genes for the biosyntheses of amino acids essential for the hosts in the genome, but those for non-essential amino acids are missing, indicating complementarity and syntrophy between the host and the symbiont. In addition, Buchnera lacks genes for the biosynthesis of cell-surface components, including lipopolysaccharides and phospholipids, regulator genes and genes involved in defence of the cell. These results indicate that Buchnera is completely symbiotic and viable only in its limited niche, the bacteriocyte.