The javax.xml.bind.JAXBElement@c89e628 phylum exclusively encompasses bacteria sharing a similar obligate intracellular life cycle. Existing 16S rDNA data support a high diversity within the phylum, however genomic data remain scarce owing to the difficulty in isolating strains using culture systems with eukaryotic cells. Yet, javax.xml.bind.JAXBElement@5026e79c genome data extracted from large scale metagenomic studies might help fill this gap. This work compares 33 cultured and 27 environmental, uncultured chlamydial genomes, in order to clarify the phylogenetic relatedness of the new chlamydial clades and to investigate the genetic diversity of the javax.xml.bind.JAXBElement@50520457 phylum. The analysis of published chlamydial genomes from metagenomics bins and single cell sequencing allowed the identification of seven new deeply branching chlamydial clades sharing genetic hallmarks of parasitic javax.xml.bind.JAXBElement@4f9dc5d2 . Comparative genomics suggests important biological differences between those clades, including loss of many proteins involved in cell division in the genus javax.xml.bind.JAXBElement@ce6c2af , and loss of respiratory chain and tricarboxylic acid cycle in several species. Comparative analyses of chlamydial genomes with two proteobacterial orders, the javax.xml.bind.JAXBElement@6b1bdea8 and the javax.xml.bind.JAXBElement@2b2b0f20 showed that genomes of different javax.xml.bind.JAXBElement@ab9fcc2 families are much more similar than genomes of different javax.xml.bind.JAXBElement@3070a480 families. On the other hand, the chlamydial 16S rRNAs exhibit a higher sequence conservation than their javax.xml.bind.JAXBElement@5abc2b8 counterparts, while chlamydial proteins exhibit increased sequence divergence. Studying the diversity and genome plasticity of the entire javax.xml.bind.JAXBElement@760a8f22 phylum is of major interest to better understand the emergence and evolution of this ubiquitous and ancient clade of obligate intracellular bacteria.