Globally, biodiversity loss is a key environmental threat caused primarily by loss of habitat and the introduction of exotic species. Australia has one of the highest extinction records in the world for mammals, with 30 mammal species now extinct. Translocations to closed systems such as fenced reserves are commonly used for the conservation of threatened fauna worldwide and although fenced reserves can provide significant conservation benefits to biodiversity, such closed systems require close monitoring. Molecular analysis of scat is increasingly being used as a non-invasive and reliable method for monitoring fauna. This presentation outlines two case studies from Western Australia with contrasting applications of molecular analysis of scats from threatened mammals. The first case study outlines the use of mammal DNA from scats as a tool for monitoring population growth and distribution in the trap shy mala (rufous hare-wallaby) in a reintroduced population. The second case study uses scat DNA to examine resource competition between two threatened mammals reintroduced into a predator-proof enclosure. The advantages of molecular analysis of scats for monitoring will be discussed as well as outlining areas where further research is required.