Members of the Anaplasmataceae genera Anaplasma, Ehrlichia, and 'Candidatus Neoehrlichia' are all tick-borne mammalian pathogens including significant animal pathogens such as E. ruminantium, and A. marginale, and severe emerging zoonotic pathogens such as A. phagocytophilum, E. chaffeensis, and ‘Candidatus Neoehrlichia mikurensis’. Only three members of these genera were thought to occur in Australia; A. platys (a canine pathogen), A. marginale (a bovine pathogen), and A. centrale (used as a live vaccine against A. marginale in cattle), each of which was introduced since European settlement, and all are vectored only by introduced tick species. In the present study we assessed the microbial populations associated with Australia’s most common native human-biting ticks, the Australian paralysis tick (Ixodes holocyclus) and the Kangaroo tick (Amblyomma triguttatum) using bacterial 16S rRNA gene profiling. Approximately 40 million partial (300 bp) bacterial 16S rRNA gene sequences were generated on the MiSeq sequencing platform, and bioinformatic analysis of these sequences revealed that four putative Anaplasmataceae species; one novel Anaplasma sp., one novel Ehrlichia sp., and two novel ‘Candidatus Neoehrlichia’ spp. were present in these native ticks. To further characterise these putative species, partial 16S rRNA gene, groESL, and gltA gene sequences were PCR amplified with genus-specific primers and sequenced. Bayesian phylogenetic reconstructions confirmed that these sequences belong to novel species that are closely related to, but distinct from previously recognised zoonotic Anaplasma, Ehrlichia, and ‘Candidatus Neoehrlichia’ species. These putative species are the first members of the Anaplasmataceae (except the benign arthropod endosymbiont Wolbachia spp.) shown to be endemic to Australia, and are of potential One Health importance due to their close relationship to many zoonotic pathogens. Like all other Anaplasmataceae pathogens, it is likely that these novel Australia species are maintained in wildlife reservoir populations through cycles of mammal-tick-mammal transmission. Research to elucidate the wildlife reservoirs as well as the potential pathogenicity of these species to animals and humans is currently being undertaken.