Australia is home to a rich biodiversity of marsupials that are found nowhere else. Unfortunately, many of these species are currently threatened with extinction due to introduced feral predators and other anthropogenic factors. There is growing recognition that host-associated microorganisms can play important roles for animal health, with billions of dollars currently being invested into human gut microbiome research and the development of microbiome-based therapeutics to improve human health. Can microorganisms also be harnessed to stem the tide of marsupial extinctions? In this review, we provide an overview of some of the challenges facing Australia's marsupials, and our current understanding of the microbiology of the marsupial pouch. We also propose outstanding research questions pertaining to the marsupial pouch, which, if addressed, may provide actionable knowledge and novel microbial therapies that could help stem the tide of marsupial extinctions in Australia.