1. Understanding the spatial structure of populations is important in developing effective management strategies for feral and invasive species, such as feral pigs Sus scrofa. World-wide, feral pigs can act as 'triple threat' pests, impacting upon biodiversity, agricultural production and public health; in Australia they are a significant vertebrate pest. We utilized a molecular approach to investigate the structure of populations of feral pigs in south-western Australia. These approaches have been underutilized in pest management. 2. Using 14 highly polymorphic microsatellite markers from 276 adult pigs, we identified eight inferred (K = 8) pig populations that would be difficult to define with standard ecological techniques. All populations had moderate heterozygosity (HE = 0.680) and moderate to high levels of differentiation (FST = 0.118; RST = 0.132) between populations. 3. The molecular approach identified feral pig groups that appeared to be acting as a source for reinvasion following control operations. It also identified populations where current control measures were less successful in reducing 'effective population size'. Additionally, the data indicated that dispersal rates between, but not within, the inferred feral pig populations were relatively low. 4. The potential for the spread of directly transmitted wildlife diseases between the pig populations studied was low. However, under some circumstances, such as within major river catchments, the role of feral pigs in the transmission of endemic or exotic diseases is likely to be high. 5. Synthesis and applications. A molecular-based approach allowed us to determine the genetic structure and dispersal patterns of a cryptic, destructive and invasive vertebrate pest. Our results indicated that the feral pig populations studied were unlikely to be acting as closed populations and, importantly, it identified where movement between groups was likely to occur. This should lead to more informed decisions for managing the potential risk posed by feral species, such as pigs, in the transmission of wildlife diseases. The suggested technique could help in understanding the dynamics of many other free-ranging pest animal populations.