The article describes the complete genome sequence of *Rickettsia prowazekii*, the causative agent of epidemic typhus, which is an obligate intracellular parasite. The genome consists of 1,111,523 base pairs and contains 834 protein-coding genes. The functional profiles of these genes show similarities to those of mitochondrial genes, with no genes required for anaerobic glycolysis found in either *R. prowazekii* or mitochondrial genomes, but a complete set of genes encoding components of the tricarboxylic acid cycle and respiratory chain complex. Many genes involved in amino acid and nucleoside biosynthesis in free-living bacteria are absent from *R. prowazekii* and mitochondria, suggesting that these genes have been replaced by homologues in the host genome. The *R. prowazekii* genome contains the highest proportion of non-coding DNA (24%) detected in a microbial genome, which may be degraded remnants of genes that await elimination. Phylogenetic analyses indicate that *R. prowazekii* is more closely related to mitochondria than any other microbe studied. The genome sequence suggests that the endosymbiotic relationship between mitochondria and α-proteobacteria may have originated from an ancestor of *Rickettsia*. The article also discusses the reductive evolution of *R. prowazekii*, including the loss of genes and the accumulation of deleterious mutations, and provides insights into the origins of mitochondria and the evolution of energy metabolism in eukaryotes.The article describes the complete genome sequence of *Rickettsia prowazekii*, the causative agent of epidemic typhus, which is an obligate intracellular parasite. The genome consists of 1,111,523 base pairs and contains 834 protein-coding genes. The functional profiles of these genes show similarities to those of mitochondrial genes, with no genes required for anaerobic glycolysis found in either *R. prowazekii* or mitochondrial genomes, but a complete set of genes encoding components of the tricarboxylic acid cycle and respiratory chain complex. Many genes involved in amino acid and nucleoside biosynthesis in free-living bacteria are absent from *R. prowazekii* and mitochondria, suggesting that these genes have been replaced by homologues in the host genome. The *R. prowazekii* genome contains the highest proportion of non-coding DNA (24%) detected in a microbial genome, which may be degraded remnants of genes that await elimination. Phylogenetic analyses indicate that *R. prowazekii* is more closely related to mitochondria than any other microbe studied. The genome sequence suggests that the endosymbiotic relationship between mitochondria and α-proteobacteria may have originated from an ancestor of *Rickettsia*. The article also discusses the reductive evolution of *R. prowazekii*, including the loss of genes and the accumulation of deleterious mutations, and provides insights into the origins of mitochondria and the evolution of energy metabolism in eukaryotes.