Interspecific hybridization leads to heterosis for growth in a significant number of forest tree genera. When it is possible to exploit this heterosis by vegetative propagation, as is currently the case in the hardwood genera Eucalyptus and Populus, interspecific hybridization is often the preferred route to genetic gain. The genetic basis of heterosis in forest trees is poorly understood, however. We have produced linkage maps of F1 and F2 interspecific hybrids in Eucalyptus and Populus, respectively, and located QTLs with major effects on stem growth, form, leaf phenology, wood quality, disease resistance, and organogenesis in vitro. Patterns of QTL inheritance for gross phenotypic traits, e.g. stem volume growth and pulp yield, have been compared with QTLs identified for physiological and anatomical correlates of these traits, e.g. sylleptic branch leaf area and wood specific gravity. Co-localization of QTLs suggests novel approaches to indirect selection in clonally propagated interspecific hybrids.