<p>The mulga complex (<i>Acacia aneura</i> and closely related taxa) is a widespread group that is dominant in much of arid Australia. The group is taxonomically difficult, due to a complex interaction of sympatry and putative hybridisation between the major species, geographic variation within species and sympatric variation within <i>A. aneura</i>. Mulga is highly variable in a wide range of vegetative and reproductive characters and it is not unusual to find five or six distinct forms growing side by side. The aim of this project was to gain a better understanding of the relationships among mulga species and <i>A. aneura</i> varieties, as well as the maintenance of this variation. A single site in the Northern Territory, containing <i>A. ayersiana, A. minyura</i> and two varieties of <i>A. aneura</i>, was sampled intensively. Six morphotypes were observed in the field and five were strongly supported by morphometric analysis. Although the mulga complex is generally tetraploid (2<i>n</i> = 52), triploid (2<i>n</i> = 39) and pentaploid (2<i>n</i> = 65) seedlings were produced in the study population. Microsatellite primers developed for <i>A. mangium</i> (sect. Juliflorae) were amplified in individuals of each morphotype, resulting in genetic marker patterns consistent with polyploidy. Genetic and morphometric distances were correlated and differences between morphotypes account for 63% of the total genetic variation (ΦPT = 0.63, <i>P</i> < 0.001). Allele sequences confirmed the presence of genuine heterozygosity and clonality was suggested by the low genotypic diversity and the lack of allele segregation. Seedlings had identical genotypes to the maternal plants and polyembryony was observed in each taxon, consistent with apomictic reproduction. Both variation of the ploidy level and apomixis may restrict gene flow among morphotypes, playing a role in the maintenance of morphological diversity at the study site. The success of the group in arid and semi-arid Australia may also be due, in part, to these factors.</p>