Intraoral disease, including macropod progressive periodontal disease, is one of the leading causes of morbidity and mortality for wallabies under human care. Clinical signs associated with intraoral disease vary, and diagnostic findings can be difficult to interpret without intraoral radiographs or advanced imaging; therefore, this disease process can be challenging to detect in its early stages. Previous studies have investigated the effects of intraoral disease on the normal oral microbiome of various domestic species. Results from these studies demonstrate specific changes to the oral microbiome that have the potential to be used as an early indicator of intraoral disease. The purpose of this study was to evaluate the oral microbiome of 12 Bennett's wallabies (Notamacropus rufogriseus) and 3 yellow-footed rock wallabies (Petrogale xanthopus), using next-generation sequencing, to determine if intraoral disease influences the oral microbiome, as demonstrated in other species. The study identified a total of 295 bacterial species and 388 fungal species from the oral cavity of 15 wallabies. Although not statistically significant, the results of the study suggest an increase in the number of anaerobic bacterial species in sites of disease, including Actinomyces bowdenii, a species from the family Propionibacteriaceae, Peptostreptococcus canis, Fretibacterium sp., and Synergistes jonesii. It also revealed a decrease in microbial diversity in animals with active intraoral disease compared with animals without active disease, as well as at the site of disease compared with the control site. Results from this study support the findings of similar studies assessing the oral microbiome of macropods. Additional studies are warranted to better understand the normal oral microbiome of Bennett's and yellow-footed rock wallabies and the dynamic changes in the microbiome that occur in animals with intraoral disease.