Technical Abstract: Ticks are considered to be second only to mosquitoes as worldwide vectors of human diseases, but they are regarded as the most relevant vectors of disease-causing microorganisms in domestic and wild animals. The cattle tick, Rhipicephalus (Boophilus) microplus, hinders livestock production in tropical and subtropical parts of the world where it is endemic. The objective of this study was to apply the bacterial 16S tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP) technique to characterize bacterial diversity in R. microplus. Pyrosequencing was performed on adult males and females, eggs, and gut and ovary tissues from adult females derived from samples of R. microplus collected during outbreaks in southern Texas. Raw data from bTEFAP was screened and trimmed based upon quality scores and binned into individual sample collections. The total number of genera identified by tick sample comprised: 53 in adult males, 61 in adult females, 11 in gut tissue, 7 in ovarian tissue, and 54 in the eggs. Genera identified that are known to include species with pathogenic effects on vertebrate or invertebrate hosts included: Wolbachia, Staphylococcus, Coxiella, Corynebacterium, Enterococcus, Pseudomonas, Clostridium, Serratia, Borrelia, Streptococcus, Klebsiella, Moraxella, Enterobacter, Shigella and Escherichia. This work contributes qualitative and quantitative data for bacteria associated with the cattle tick R. microplus. Bacteria harbored by the cattle tick with the potential to be pathogenic to vertebrate hosts were identified. This report represents the first comprehensive survey of the bacteriome in the cattle tick using non-culture based molecular approaches.