Most theories to explain the origin and maintenance of clines in Eucalyptus are based on a morphological classification system. The true relationships between putative species along clines require detailed investigation of phylogenetic relationships. A cline between Eucalyptus melanophloia and E. whitei was examined using morphological and molecular analyses to determine whether genetic structuring in nuclear and chloroplast DNA along the cline could be explained by secondary contact between independent evolutionary lineages, or whether the cline represents a single species that has undergone primary differentiation. Morphological analysis showed phenotypic variation distributed continuously across the cline and that seedlings bred true to parental type. Microsatellite analysis indicated that there was little genetic structuring across the cline, and low levels of population differentiation. This result was further reinforced by analysis of the cpDNA. The phylogeographic distribution of cpDNA haplotypes is likely to have resulted from restricted seed-mediated gene flow with isolation by distance. A cogent explanation for the cline is that it has arisen by selection on leaf types promoted by a gradient in precipitation with the short-broad, subsessile leaves of E. melanophloia favoured under higher rainfall and the long, narrow, petiolate leaves of E. whitei favoured in arid environments.