Vegetative propagation by stem cuttings and mini-cuttings has been used worldwide for growing Eucalyptus plants. However, clones and hybrids of this plant present a great variability in their rooting capacity, apart from a gradual decrease in the rooting potential due to the ontogenetic age of the mother plant. Several studies have demonstrated that some bacteria promote plant growth and rooting through the action of direct and indirect mechanisms that are not still completely clear. Considering this, the objective of this study was to assess the production of auxins, abscisic acid and siderophores in Bacillus subtilis and Stenotrophomona maltophilia, which in previous studies increased rooting of E. globulus cuttings. Additionally, the population of these bacteria in the rhizosphere, superficial tissues of the stem-base and callus of the mini-cuttings was identified, and quantified by real-time PCR. Only S. maltophilia produced IAA in the presence of tryptophan; none of the bacterial strains produced ABA, but both produced siderophores. A comparative analysis of the separation profiles showed that there is a diverse microbial community in the rhizosphere, and only S. maltophilia was capable of keeping its population at a density of 2.03 × 10(7) cells/mg in different tissues of the mini-cuttings. The results would indicate that the rooting stimulus in E. globulus could be related to the action of one or several mechanisms such as the production of auxins and siderophores, and it could also be associated with the ability of bacteria to stay in the rhizosphere or in plant callus tissues.