* Formylated phloroglucinols (FPCs) are key defensive compounds that influence herbivory by mammals and arthropods in eucalypts. However, the genetic architecture underlying variation in their levels remains poorly understood. * Quantitative trait loci (QTL) analysis for the concentrations of two major FPCs, sideroxylonal A and macrocarpal G, was conducted using juvenile leaves from 112 clonally duplicated progenies from an outcross F2 of Eucalyptus globulus. * Two unlinked QTL were located for macrocarpal, while another unlinked QTL was located for sideroxylonal. The sideroxylonal QTL collocated with one for total sideroxylonal previously reported using adult Eucalyptus nitens foliage, providing independent validation in a different evolutionary lineage and a different ontogenetic stage. * Given the potential widespread occurrence of these QTL, their ontogenetic stability, and their impact on a range of dependent herbivores, it is possible that they have extended phenotypic effects in the Australian forest landscape.