The loss of many small and medium mammal species from eastern Australia during the 19th and early 20th centuries greatly outpaced scientific collection or preservation of live-caught specimens for other purposes. Bounties, diaries and newspaper reports provide conclusive evidence of the former distribution of some readily-diagnosed larger bodied species. However, to establish the distribution of small-bodied species such as mice, the only known viable source of information is bone accumulations associated with owl roosts. These deposits also provide potential to determine population genetics and isotopic analyses of dietary shifts, along with tracking natural community changes through pre-historical environmental changes. These deposits record the clear decimation of small mammal faunas across eastern Australia in the wake of European colonisation. Here we discuss the case study of southern highland faunas and an ecological restoration project at Mulligans Flat in the Australian Capital Territory, as well as broader patterns of interest across eastern Australia. Owl pellet deposits were essential in determining species that were suitable for reintroduction into the feral predator-proof fenced area of Mulligans Flat. The fauna revealed by deposits in and around the ACT was far richer than faunal lists suggested. However, like the loss of knowledge that occurred with the passing of early settlers who lived with these species, many bone deposits are prone to disturbance, and are themselves now at risk of being lost.