DNA analyses of wildlife can provide valuable diagnostic tools and have direct application to the study of ecological and other environmental phenomena. Yet, well documented and tested markers exist for only a handful of species. One of the reasons for this is that good sequence information and robust sampling at the appropriate level of resolution is lacking for many taxa. We report on the development of DNA markers that enable us to detect red foxes from trace samples such as scats (faeces) in Australia and then use genotype-by-sequencing and a citizen science based collection of tissue samples to conduct a continental analysis that recapitulates the invasion sequence of red foxes into Australia. We demonstrate that technologies have the potential to substantially enrich our knowledge of mammalian ecology but that the development of comprehensive and good quality tissue collections matched to accurate locational information, better marker resolution, regular repeat collections of DNA samples, high quality sequences in online databases, and minimisation of laboratory errors are the key to maximising that potential.