Ecological factors are important drivers of phenotypic divergence, which may lead to incipient speciation. A variety of habitats should be preserved to maintain evolutionary potential. We used the marsupial, the yellow-footed antechinus (Antechinus flavipes) as a model species for investigating phenotypic differentiation between animals inhabiting two habitat types in south-eastern Australia: flood-plain river red gum and box–ironbark forests. All tested phenotypic characteristics varied between years at the same sites and therefore were not useful for investigating morphological specialization that may lead to speciation. Males generally were significantly heavier when antechinus densities were lower, but exceptions were found, possibly related to food availability. Teat-number variation recently has been shown to be associated with habitat specialization and incipient speciation within Antechinus agilis. We investigated genetic differentiation associated with this trait in A. flavipes. Population genetic analyses of microsatellite genotypes and mitochondrial DNA haplotypes revealed that sympatric 12-, 13- and 14-teat females in Chiltern forest were part of one freely interbreeding population. Our parentage analyses found two cases where 13-teat mothers produced 12-teat daughters. This suggests either plasticity or paternal genetic influence on the offspring's teat-number phenotype. Laboratory matings may be required to resolve the extent to which teat number is heritable in A. flavipes. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 94, 303–314.