Recent technological advances have resulted in a dramatic renaissance of population genetics and its application to species ecology and conservation. This review summarizes the progress made in applying these new techniques, notably hypervariable genetic markers (microsatellite loci and mitochondrial control region), to the study of marsupials. Since 1990, population genetic studies have overwhelmingly been of marsupial species from eastern and southern Australia, largely focusing on threatened species or those with restricted distributions. To date, over 500 polymorphic microsatellite loci have been isolated from 38 marsupial species (6 American, 32 Australian), including representatives from 13 of the 18 extant marsupial families. Levels of microsatellite diversity identified within the 209 marsupial populations (43 species) so far examined have varied greatly, although the range is similar to those reported from eutherians and other vertebrates. Marsupial populations with high levels of genetic diversity tend to be those from relatively abundant or widespread species, while those with lower levels are typically species with restricted distributions, that are threatened, found on islands or have been established via translocation. Although data for most families are still limited, bandicoots, koalas and wombats appear less and phalangerids more diverse than the marsupial average. The application of these hypervariable genetic markers to investigate marsupial species ecology has substantially improved our understanding of population biology, behaviour and reproduction in many species, as well as informing conservation initiatives and management plans for many threatened marsupial taxa. It is hoped that in the future, marsupial population genetic studies can be expanded to include a larger number of South American and New Guinean species, as well as a better representation of arid, tropical, widespread and abundant Australian species.