The Acacia acuminata complex is a group of woody shrubs and small trees comprised of three formally described taxa (A. oldfieldii, A. acuminata ssp. acuminata and ssp. burkittii) and two informal taxa ("small seed" and "narrow phyllode") with contrasting geographical distributions within the south-west of Western Australia. In addition, a series of variant populations of possible hybrid origin exist. Population genetic structure was investigated in 25 populations representing the taxa and variants using 16 polymorphic allozyme loci. All taxa and variants exhibited relatively high levels of genetic variation compared with other woody angiosperms with similar geographic distributions. Levels of genetic diversity in the widely distributed ssp. burkittii and "narrow phyllode" taxon were considerably higher (H(e), 0.311 and 0.319, respectively) than expected for widespread woody shrubs. In contrast, the rare and highly restricted A. oldfieldii exhibited significantly lower levels of genetic diversity (H(e), 0.173) compared with the other taxa in the complex, but higher than other rare woody shrubs. Although morphologically close, associations based on genetic distance showed A. oldfieldii was highly divergent from the other taxa (D = 0.85) while including variant populations confused systematic alliances. The unusual placement of some of these populations and high degree of population differentiation (G(ST), 12.7%) supports the suggestion that these may represent a series of hybridisation events between the various taxa.