High densities of introduced herbivores can damage sensitive ecosystems, increase the risk of extinction of native biota, and host and spread disease. An essential step in managing large ‘feral’ animal populations is to quantify how they use habitats so that management interventions, such as culling, can be targeted to reduce densities and to minimize migration into areas from which animals have been removed. An effective method to quantify animal movements is by measuring landscape-scale genetic population structure. We describe the genetic population structure of one of Australia's more destructive introduced mammals – the Asian swamp buffalo (Bubalus bubalis). We collected 524 skin samples from buffalo across their range in the Northern Territory of Australia. Allelic diversity in the Northern Territory population was low compared to those reported from populations in their native Asian habitats. The Australian population is tentatively made of three subpopulations; Melville Island, Eastern Arnhem and Central-Western Arnhem populations. The Melville Island population is represented by a single cluster, while the Eastern Arnhem population has three clusters and the Central-Western Arnhem population seven clusters. We found some support for isolation by distance across all the sampled populations, but little evidence for this relationship when comparing the two well-mixed mainland meta-populations. Despite their small founder populations and limited genetic variation, the persistence of buffalo in Australia has likely been aided by release from high predation, parasitism and disease typical of their native habitats.