Few studies have described the genetic diversity within and between populations of polyploid plant species despite the general acceptance of the importance of polyploidy in plant diversification and speciation. The genus Atriplex has a complex evolutionary history in Australia that has included polyploidy and hybridization among perennial forms. The octoploid, dioecious species Atriplex nummularia is proposed to have evolved from an octoploid ancestor in the coastal semi-arid fringe of south-western Australia, and to have spread east and diversified into taxa which occupy edaphically different habitats. Despite interest in the diversification of the genus, and the ecological and economic importance of A. nummularia, there are no descriptions of the genetic structure of the species. Nuclear microsatellite markers and principal coordinate analysis, analysis of molecular variance, Bayesian and phenetic analyses were used to investigate the diversity and taxonomic relationships of two common subspecies of A. nummularia. Genetic diversity was high overall (A = 509, A′ = 42.4, Ho = 0.824, H′ = 2.8), but values were significantly lower in the western subspecies, A. nummularia ssp. spathulata. As in other outbreeding, perennial species, most of the genetic diversity was within populations (FST = 0.125). Clear divergence of subspecies was evident in principal coordinate analysis, neighbor-joining and Bayesian clustering analyses and the differentiation of populations was very low within subspecies (FSC = 0.048). These findings support the taxonomic separation of the two subspecies. Clustering patterns based on Bayesian analyses suggested that the polyploid subspecies of A. nummularia have multiple origins. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105, 218–230.