The understanding of the biochemical changes that occur during the different phases of rooting makes it possible to obtain higher percentage microshoots rooting in woody species. To differentiate the two species and find a marker rhizogenic capacity in the present study is to characterize kinetic profile of Indole Acetic Acid content (AIA), total phenols and total carbohydrates. To this microshoots species Eucalyptus nitens (H. Deane & Maiden) Maiden and Eucalyptus globulus Labill. which were evaluated were treated with the method of the slow induction of rooting on Murashige & Skoog (1962) (MS) with the salts in half, supplemented with auxin naphthaleneacetic acid (NAA) for 7 days in darkness. Subsequently transferred to sterile vermiculite substrate irrigated crop MS medium without hormones. Plant materials on days 0, 2, 7 and 20 days from the induction manifolds, core samples were taken cuttings for analysis phytochemicals. The AIA on days 0 and 2, showed high values decreased dramatically during the next phases of rooting days 7 and 20. Phenolic compounds showed differences between the two species evaluated in time, with significantly higher values in Eucalyptus nitens (136 ug/gPS) in E. globulus (29 ug/gPS), total carbohydrates showed no differences between species and stay high all the time The AIA is essential for induction of rooting and is not subsequently required, as carbohydrates are not candidates for markers rhizogenic capacity not because they differ in the two species of Eucalyptus. According to the obtained phenolic compounds are good markers of the capacity of adventitious rooting since differed significantly in the two species of Eucalyptus.