The control of foxes (Vulpes vulpes) is a key component of many fauna recovery programs in Australia. A question crucial to the success of these programs is how fox control influences feral cat abundance and subsequently affects predation upon native fauna. Historically, this question has been difficult to address because invasive predators are typically challenging to monitor. Here, non-invasive DNA analysis was used to determine the fate of radio-collared woylies (Bettongia penicillata) in two reserves in a mesic environment where foxes had been controlled intensively for over two decades. Woylie trap success had increased more than 20-fold after fox baiting commenced in the 1980s but decreased precipitously in 2000. Ninety-eight monitored woylies were killed between 2006 and 2009. DNA analysis of swabs taken from radio-collars and carcasses of these woylies indicated that predation by cats (Felis catus) caused most mortalities (65%) and was three times the fox predation rate (21%). Also, indices of cat abundance were higher in fox-baited sites where foxes were less abundant. Predation on woylies by cats was greater than previously recognised and, by implication, may significantly reduce the effectiveness of fox control programs throughout Australia. Integrated fox and cat control is essential to ensure the success of fauna recovery programs.