SummaryPlant cuticular wax compounds perform functions that are essential for the survival of terrestrial plants. Despite their importance, the genetic control of these compounds is poorly understood outside of model taxa. Here we investigate the genetic basis of variation in cuticular compounds inEucalyptus globulususing quantitative genetic and quantitative trait loci (QTL) analyses.Quantitative genetic analysis was conducted using 246 open‐pollinated progeny from 13 native sub‐races throughout the geographic range.QTLanalysis was conducted using 112 clonally replicated progeny from an outcross F2population.Nine compounds exhibited significant genetic variation among sub‐races with three exhibiting signals of diversifying selection. Fifty‐twoQTLwere found with co‐location ofQTLfor related compounds commonly observed. Notable among these was theQTLfor five wax esters, which co‐located with a gene from theKCSfamily, previously implicated in the biosynthesis of cuticular waxes in Arabidopsis.In combination, theQTLand quantitative genetic analyses suggest the variation and differentiation in cuticular wax compounds withinE. globulushas a complex genetic origin. Sub‐races exhibited independent latitudinal and longitudinal differentiation in cuticular wax compounds, likely reflecting processes such as historic gene flow and diversifying selection acting upon genes that have diverse functions in distinct biochemical pathways.