Eucalyptus globulus Labill. is the premier hardwood plantation species in temperate regions of the world. We developed twelve E. globulus microsatellite loci for fingerprinting and future studies in genome mapping, gene flow and genetic diversity. The microsatellites were highly polymorphic in E. globulus (average number of alleles per locus, 17.8; average observed heterozygosity, 0.66). The loci were robust, amplifying in other Eucalyptus species, Corymbia and Angophora. The high variability and transferability of these molecular markers make them useful in E. globulus, as well as in many of the 700 species of Eucalyptus.