Animals are reliant on their gut microbiota for health and well-being, but surprisingly, little microbiome research has been conducted on the iconic Australian fauna. This includes marsupials from the order Diprotodontia; koalas, kangaroos, possums and wombats. These animals have a varied diet of leaves, grasses and insects but particularly interesting are those that are able to digest a toxic Eucalypt diet, such as the koala, greater glider, common brushtail and ringtail possum. This dietary diversity leads to the question of whether marsupial evolution or diet drives microbial community composition in these animals. To answer this question we collected 94 faecal samples from 17 genera and 23 species belonging to the order Diprotodontia and investigated their microbiomes using metagenomics and metabolomics. An additional 23 faecal samples were sequenced using proximity ligation (Hi-C) sequencing to identify associations between viruses, plasmids and their microbial hosts. A total of 3,868 MAGs (>70% complete) were extracted and combined with public genomes for community profiling. Principal component analysis revealed that host phylogeny was the main driver of faecal microbial community composition. From the Hi-C sequencing data, 6,040 MAGs (many <50% complete) were associated with viruses and 167 MAGs were associated with plasmids. The genus Faecousia was associated with the greatest number of phages per genome, being present in all kangaroo and wallaby samples but absent in other marsupial species. The metabolomics data showed that eucalypt terpenes were unmodified, however there was an increase in fatty acids, inferred to be the result of microbial metabolism.