The One Health concept emphasizes the interdependence of human, animal, and environmental health. The microbial components (microbiomes) of these ecosystems play essential roles in maintaining health, however, in many cases we still lack even a basic knowledge of these microbiomes. In this study, we investigated the gut microbiomes of a wide range of Australian marsupials using shotgun metagenomics, providing the first such data for many of these species. From 94 faecal microbiomes metagenomes spanning 25 different Australian marsupial species and 17 genera, we obtained 1,096 medium quality metagenome-assembled genomes (MAGs) (dereplicated at 95% ANI) of prokaryotic gut species. Marsupial hosts had characteristic gut microbiomes that largely reflected host phylogeny. Adaptation to a eucalyptus diet in koala, greater glider and some possum species appears to have arisen independently via convergent evolution. These data provide a baseline of microbial information for marsupial species, which remain understudied with respect to their microbiomes. Our results showed no gut species exclusively found in eucalyptus feeders, suggesting that adaptations to this diet may be due to different organisms having the same function.