Uninformed management decisions have the potential to create significant problems for conservation programs. In the south-western corner of Australia where conservation initiatives are directed towards restoring large tracts of land degraded by broadscale clearing and increasing levels of dryland salinity, Melaleuca uncinata R.Br. (Myrtaceae) is a species complex of considerable interest for restoration. Although M. uncinata is morphologically uniform across most of southern mainland Australia, there is considerable variation in south-western Australia and a recent morphological evaluation has recognised 11 species. Phylogenetic patterns among populations of seven of these species were examined with nuclear RFLP loci to determine whether morphological and phylogenetic boundaries were congruent before the implementation of any broadscale revegetation programs. The phylogenetic analysis was congruent with the morphological assessment, and populations of different species, including those co-occurring at the same site, clustered according to their correct morphological assignment. Some genetic structuring associated with habitat preference was also evident within two of the species. The taxonomic resolution and knowledge of the phylogenetic relationships among the seven species will facilitate their further assessment for issues relevant to revegetation, such as provenance and local adaptation. It will also enable selection of appropriate germplasm in revegetation programs to maximise the genetic adaptation in restoration and minimise negative impact of plantings on remnant vegetation.