Animal cells are the sole habitat for a variety of bacteria. Molecular
sequence data have been used to position a number of these intracellu
lar microorganisms in the overall scheme of eubacterial evolution. Mos
t of them have been classified as proteobacteria or chlamydiae. Here w
e present molecular evidence placing an intracellular symbiont among t
he flavobacteria-bacteroides. This microorganism inhabits specialized
cells in the cockroach fat body and has been described as a mutualisti
c endosymbiont of uncertain phylogenetic position. The small subunit r
ibosomal DNA of these bacteria was analysed after polymerase chain rea
ction 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 f
lavobacteria. In addition, the relationships among the endosymbionts,
as revealed by DNA sequence data, appeared to be congruent with the ho
st taxonomic relationships. Based on the host fossil record, a tentati
ve calibration of the nucleotide substitution rate for the cockroach f
lavobacteria gave results congruent with those obtained for the aphid
endosymbiotic proteobacteria.