Recent advances have transformed the field of population genetics and lead to a dramatic renaissance in the application of these techniques to the study of ecology and conservation. We review the progress made in applying these tools, notably hypervariable genetic markers (microsatellite loci and mitochondrial control region) and new statistical methods, to the study of wild macropodoid populations. Population genetic studies have been conducted on 20 macropodoid species, more species than any other marsupial group, although most studies have focussed on threatened species or those with restricted distributions. A substantial number of microsatellite loci (n = 79) have been isolated from seven macropodoid species, which have been used to successfully amplify polymorphic loci in representatives of all three extant macropodoid families and most genera. Levels of microsatellite diversity identified within the 61 macropodoid populations so far examined have varied enormously, although the range of values is similar to those reported from eutherians and other vertebrates. Macropodoid populations with high levels of genetic diversity tended to be those from relatively abundant or widespread species, while those with lower levels were typically from species with restricted distributions, that are threatened, found on islands or have been established via translocation. The level of genetic structuring among macropodoid populations was variable, but consistent with known species biology. Limited structure has been documented in widespread, vagile species such as kangaroos, while moderate or high amounts of genetic structure were found in habitat specialists, such as rock-wallabies. Studies to date suggest that dispersal for macropodoids is male-biased, which is broadly consistent with behavioural observations. Although the power to detect fine-scale genetic sub-structuring within a population has only recently become available, two studies have independently detected a pattern of differential spatial structuring between male and female rock-wallabies within single colonies. This suggests strong female philopatry and that within-colony dispersal is also male-biased. Data on the genetic mating systems of macropodoids in the wild are available for only four species. These studies have largely confirmed behavioural-based mating system hypotheses but have also shed light on alternative mating strategies. The potential of hypervariable genetic markers to investigate ecological patterns has been powerfully demonstrated within wild macropodoid populations. These studies have improved our understanding of macropodoid population biology, behaviour and reproduction, as well as informing conservation initiatives and management plans for many threatened macropodoid taxa. It is hoped that in the future, population genetic studies can be expanded to include a larger number of widespread and abundant macropodoid species, especially those in northern Australia that have been less severely impacted by European settlement.