The evolutionary potential of plant species that reproduce via predominantly clonal means and the conditions under which clonality is favoured are not well known. Long-term clonal reproduction is expected to result in a number of readily detectable genetic signals not present in populations that reproduce by sexual means. We use a hierarchical sampling strategy to assess genotype probabilities and confirm that two rare sister taxa of Banksia ionthocarpa have contrasting modes of reproduction. Banksia ionthocarpa subsp. chrysophoenix reproduces clonally. Populations had low levels of genotypic diversity and were comprised of large clonal patches consisting of many ramets that covered hundreds of square metres and showed little intermixing. The taxon was genetically depauperate (mean Na = 1.97, mean P = 0.66, mean He = 0.282), had high levels of genetic differentiation between populations (θ = 0.481), and populations exhibited excess heterozygosity and linkage disequilibrium (LD) among loci, suggesting historically high levels of clonality. In contrast, the sister taxon B. ionthocarpa subsp. ionthocarpa, which occurs in an area with more than twice the annual rainfall and less extreme minimum and maximum temperatures, showed no evidence of clonality, high levels of genotypic diversity, greater genetic diversity (mean Na = 3.31, mean P = 0.81, mean He = 0.405), lower levels of genetic differentiation between populations (θ = 0.253) and no evidence of excess heterozygosity or LD among loci. We suggest that the development of clonality in subsp. chrysophoenix is associated with its more marginal environment and enhanced by response to recurrent fires.