Phylogenetic relationships of Xenorhabdus spp. and Photorhabdus sp. were investigated on the basis of 16S rRNA gene sequences. Xenorhabdus spp. and Photorhabdus sp. were grouped together with Proteus vulgaris and Arsenophonus nasoniae. This group was distant from other members of the family Enterobacteriaceae. Xenorhabdus japonicus, previously proposed as a new species, was nearly located to Xenorhabdus nematophilus. Signature nucleotides of X. japonicus were identified that distinguish it other members of the family Enterobacteriaceae.