Ticks are arthropods that can host and transmit pathogens to wild animals, domestic animals, and even humans. The bacterial microbiome of adult (males and females) and nymph Rhipicephalus microplus ticks collected from a collared peccary, Pecari tajacu, captured in the rural area of Botijón Village in the Amazon region of Madre de Dios, Peru, was evaluated using metagenomics. The Chao1 and Shannon–Weaver analyses indicated greater bacterial richness and diversity in female ticks (GARH; 375–4.15) and nymph ticks (GARN; 332–4.75) compared to that in male ticks (GARM; 215–3.20). Taxonomic analyses identified 185 operational taxonomic units representing 147 bacterial genera. Of the 25 most prevalent genera, Salmonella (17.5%) and Vibrio (15.0%) showed the highest relative abundance followed by several other potentially pathogenic genera, such as Paracoccus (7.8%), Staphylococcus (6.8%), Pseudomonas (6.6%), Corynebacterium (5.0%), Cloacibacterium (3.6%), and Acinetobacter (2.5%). In total, 19.7% of the detected genera are shared by GARH, GARM, and GARN, and they can be considered as the core microbiome of R. microplus. To the best of our knowledge, this study is the first to characterize the microbiome of ticks collected from P. tajacu and to report the presence of Salmonella and Vibrio in R. microplus. The pathogenic potential and the role of these bacteria in the physiology of R. microplus should be further investigated due to the possible implications for public health and animal health in populations neighboring the habitat of P. tajacu.