Tasmanian devil populations have declined up to 95% in parts of Tasmania due to the infectious cancer, Devil Facial Tumour Disease (DFTD). In 2003, the Save the Tasmanian Devil Program (STDP) was established to address this threat. Initial research included investigation into the disease, its transmission, latency and potential causes. Genetic research has contributed much to our current understanding of DFTD and the devil’s capability to respond to the disease. Using the Tasmanian devil genome (published in 2012) we have been able to develop species-specific genetic assays targeted to certain regions of the genome, particularly the immune region. These assays have not only been used to answer valuable disease related research questions but also for conservation management purposes. Our research has used these assays to: determine founder relationships of the insurance metapopulation and the consequences for the breeding program; reconstruct the Maria Island pedigree improving island management; genetically assess incumbent wild populations and select the most genetically appropriate individuals for release; and develop novel methods to utilise citizen science to enhance our understanding of the different genetic diversity across Tasmania, in particular the inaccessible south-west, by asking hikers to collect scat samples. We have integrated our conservation genomic research with real-time feedback to the STDP management team who are responsible for the long-term survival of this iconic endangered species. Our approach of trolling the genome to develop tools to answer a variety of evolutionary, disease and ecological questions has direct applications to other endangered species globally.