Plant secondary metabolites (PSMs) mediate a wide range of ecological interactions. Investigating the effect of environment on PSM production is important for our understanding of how plants will adapt to large scale environmental change, and the extended effects on communities and ecosystems. We explored the production of PSMs under elevated atmospheric carbon dioxide ([CO(2)]) in the species rich, ecologically and commercially important genus Eucalyptus. Seedlings from multiple Eucalyptus globulus and E. pauciflora populations were grown in common glasshouse gardens under elevated or ambient [CO(2)]. Variation in primary and secondary chemistry was determined as a function of genotype and treatment. There were clear population differences in PSM expression in each species. Elevated [CO(2)] did not affect concentrations of individual PSMs, total phenolics, condensed tannins or the total oil yield, and there was no population by [CO(2)] treatment interaction for any traits. Multivariate analysis revealed similar results with significant variation in concentrations of E. pauciflora oil components between populations. A [CO(2)] treatment effect was detected within populations but no interactions were found between elevated [CO(2)] and population. These eucalypt seedlings appear to be largely unresponsive to elevated [CO(2)], indicating stronger genetic than environmental (elevated [CO(2)]) control of expression of PSMs.