Emerging zoonotic diseases are one of the main threats to human and animal health. Among the agents with the potential for zoonoses, those of bacterial origin have great relevance in Public Health. Rodents are considered one of the main reservoirs of pathogens that represent a risk to human health or animal species. We used massive 16S ribosomal RNA gene amplicon sequencing to survey bacteria present in the spleen of six species of rodents in Panama in order to identify bacterial taxa with zoonotic potential in the country. We found 3352 bacterial Amplicon Sequence Variants (ASVs, i.e., phylogenetic species) in the spleen of six rodent species surveyed (Liomys adspersus, Melanomys caliginosus, Mus musculus, Proechimys semispinosus, Rattus rattus, Zygodontomys brevicauda). This bacterial community was represented by 25 phyla, 55 classes, 140 orders, 268 families, and 508 genera. The three predominant phyla were Actinobacteria, Firmicutes, and Proteobacteria, and the five predominant classes were Actinobacteria, Alpha- and Gammaproteobacteria, Bacilli, and Clostridia. There were seven high-abundance genera: Acinetobacter, Bartonella, Cutibacterium, Enterococcus, Sarcina, Staphylococcus, and Wolbachia. Genera found with less abundance included Bradyrhizobium, Chryseobacterium, Clostridium, Corynebacterium, Lactobacillus, Pseudonocardia, Rhodococcus, and Sphingomonas. Some of these genera (high or low abundance) have clinical importance. The identification of bacterial taxa with zoonotic potential in rodent species performed here allows us to have surveillance mechanisms for these pathogens and to be able to recognize localities to be prioritized for prevention of transmission and outbreaks, thus being of value for public health in Panama.