Little is known about the bacterial communities within ticks that parasitise horses and their pathogenic potential in Australia. Therefore, the aim of this present study was to identify and characterise the bacterial communities of ticks removed from horses in Australia. Seventy ticks were morphologically identified using standard identification keys from 42 horses from three states in Australia (New South Wales, Queensland, and Western Australia). Six tick species were identified, which included Amblyomma triguttatum (n = 13), Haemaphysalis longicornis (n = 22), H. bancrofti (n = 9), Ixodes holocyclus (n = 23), I. tasmani (n = 1), and Rhipicephalus australis (n = 2). Following DNA extraction of the ticks, next generation 16S rRNA metagenomic sequencing was conducted using the Illumina MiSeq platform. Over 4 million sequences were obtained, which included environmental, endosymbiotic, and potentially pathogenic bacterial genera. The most abundant bacterial sequences obtained were bacterial endosymbionts of ticks: Coxiella sp. (H. longicornis), Rickettsia sp. (H. bancrofti), Francisella sp. (A. triguttatum), and "Candidatus Midichloria mitochondrii" (I. holocyclus). Bacteria genera of interest included Rickettsia spp., which were detected in I. tasmani and R. australis ticks, but these genera could not be resolved to the species level. This study illuminates the diversity of bacterial genera residing in ticks that parasitise horses and may be of medical and veterinary importance.