During periderm differentiation, phellem cells undergo secondary cell wall thickening by suberin deposition, forming a compact barrier shielding plant organs from the environment. Development and suberization of periderm cells are tightly controlled processes, however their regulation is still poorly understood. To identify novel regulators of these processes, we have conducted histological and transcriptomic analyses to follow periderm development in two model systems: Arabidopsis and cork oak (Q. suber). After a detailed spatio-temporal study of periderm formation in Arabidopsis roots, a transcriptomic analysis using TRAP-Seq targeting periderm cells at the onset of suberization was performed with the aim to identify tissue-specific regulators. We found 2433, out of 4631 differentially expressed genes overrepresented in suberizing cells. Through a functional enrichment analysis, several terms were found to be represented, as suberin biosynthesis, response to karrikin, cell wall metabolic process and response to abscisic acid. Possible candidate genes involved in control of phellem suberization will be identified and selected for further functional validation. Furthermore, in cork oak, histochemical analyses on 1-week old tap roots, showed a positive effect of drought and heat stress on periderm development. This system is now being used as a model to identify regulators of cork formation in this species. A comparative transcriptomic analysis based on different growth conditions and root differentiation stages was performed, revealing contrasting transcriptome changes between different root zones. Genes potentially involved in the crosstalk between cork development and response to environmental changes are being identified by integrating the results obtained from both plant systems. This knowledge might further contribute to design new strategies for the improvement of cork production under abiotic stress conditions.