Dental disease is the most common presenting complaint in pet chinchillas (Chinchilla lanigera) in clinical practice. In contrast to rabbits and guinea pigs, chinchillas also suffer frequently from periodontal disease, caries, and tooth resorption. Clinical bacterial cultures are less commonly collected from chinchillas with dental disease because of the lower incidence of grossly obvious odontogenic abscesses. Therefore, the prevalence of predominant bacterial isolates in chinchillas with periodontal infections is currently unknown. Antimicrobial choices are more often made based on extrapolation from other species. Given the different presentations between chinchillas and other hindgut fermenters, the objective of our work was to evaluate the most common bacterial species present in the oral cavities of chinchillas - those with and without dental pathology. A total of 22 chinchillas presenting to two specialty referral exotic animal clinics were sampled by swabbing the oral cavity (in healthy animals) or the periodontal purulent discharge of those with disease. The samples were evaluated using next-generation DNA sequencing to detect bacterial species. The most common isolates in healthy animals were Streptococcus spp. In animals with periodontal disease, Streptococcus spp. and Fusobacterium spp. predominate. This data will help clinicians guide empirical antimicrobial choices for chinchillas with periodontal disease.