Berberis buxifolia is a Patagonian shrub with great economic potential for tinctorial, pharmacological, and food industries. Clonal propagation is possible through in vitro culture and is also useful for metabolite production. However, this species is difficult to root, and to improve this, more knowledge of rhizogenesis processes is needed. Polyamines and peroxidases are useful biochemical markers during analysis of rooting phases for correlation with tissue morphological changes. Therefore, endogenous polyamine (putrescine, spermidine, spermine) changes, peroxidase activity evolution, and morphological development were studied to characterise the in vitro rhizogenesis of microshoots of B. buxifolia and, thus, to define the rooting phases. Polyamine and peroxidase changed significantly during the rooting period, and had opposite behaviours which were directly related to the IBA media content. The lower polyamine concentration and the higher peroxidase activity were found in a treatment with a dark period during the first four days and with IBA in the culture medium. Putrescine was the most abundant polyamine found in B. buxifolia tissues, 14-to 18-fold more than spermidine and spermine, respectively. Therefore, these compounds were used to define the rooting phases: an induction phase (0 to 4-7 days) followed by an expression phase (4-7 to 28 days). The observed changes in the biochemical markers could be correlated with microscopic and macroscopic tissue observations in the microshoots, and the time course of rooting percentage. Successive culture media can be developed including polyamines, or other compounds and environmental conditions, which positively modify the studied biochemical markers behaviour.