Reintroduction is a key conservation tool, particularly in Australia where predation by introduced feral cats (Felis catus) and red fox (Vulpes vulpes) have extirpated many species from much of their distributions. While establishment of populations is often the focus, the trophic interactions and impacts of reintroduced species on existing species requires attention if conservation actions are to be effective in the long term. The Mulligans Flat Woodland Sanctuary (MFWS) in the Australian Capital Territory, Australia has facilitated the reintroduction and establishment of a range of mammals, including the eastern quoll (Dasyurus viverrinus) and eastern bettong (Bettongia gaimardi) to threatened Box-gum grassy-woodland habitat. We used next-generation sequencing of faecal samples to assess the diet of these two species to understand how they interact with, and potentially impact on the ecosystem. This approach identified unexpected trophic interactions and diet preferences in these two species. Eastern quolls consumed a larger than expected variety of vertebrate prey, while the eastern bettongs were shown to be consuming a range of geophytic and tuberous plant species, but only at certain times of year. Understanding the diet of reintroduced populations, particularly where species are contained within fenced sanctuaries, is critical to the long-term success of conservation translocations. The application of genomic tools, combined with ecological data at MFWS is providing information critical to our understanding of these reintroduced species and their trophic interactions that can enhance ongoing management.