Animal cells are the sole habitat for a variety of bacteria. Molecular sequence data have been used to position a number of these intracellular microorganisms in the overall scheme of eubacterial evolution. Most of them have been classified as proteobacteria or chlamydiae. Here we present molecular evidence placing an intracellular symbiont among the flavobacteria-bacteroides. This microorganism inhabits specialized cells in the cockroach fat body and has been described as a mutualistic endosymbiont of uncertain phylogenetic position. The small subunit ribosomal DNA of these bacteria was analysed after polymerase chain reaction amplification to investigate their phylogeny. The endosymbionts of five species of cockroaches were found to make up a coherent group with no close relatives within the eubacterial phylum defined by the flavobacteria. In addition, the relationships among the endosymbionts, as revealed by DNA sequence data, appeared to be congruent with the host taxonomic relationships. Based on the host fossil record, a tentative calibration of the nucleotide substitution rate for the cockroach flavobacteria gave results congruent with those obtained for the aphid endosymbiotic proteobacteria.