Matrilineal population structure, or male-biased dispersal among female kin groups, is typical of many eutherian mammals. In contrast, matrilineal genetic structuring has not been well documented in marsupials, although recent studies on the brush-tailed rock-wallaby are suggestive of the presence of female kin groups within colonies. We used spatial patterns of mitochondrial DNA (mtDNA) variation and long-term mark-recapture records to examine patterns of population structure and dispersal within and among brush-tailed rock-wallaby colonies in southeastern Queensland. We test the following two hypotheses: that strong female philopatry has led to lineage sorting among neighbouring brush-tailed rock-wallaby colonies and that female rock-wallabies form kin groups within a single colony. We documented unique haplotypes within most colonies, with strong and significant population structuring (high ΦST values) among colonies within two neighbouring valleys. In addition, females sharing mtDNA haplotypes formed tight and significant spatial clusters along only 800m of cliff line within a single colony; however, no such spatial clustering was found for males. These findings further demonstrate that female brush-tailed rock-wallabies are faithful to their natal colony and provide support for the presence of kin groups in a marsupial.