Aiming at the establishment of a breeding program based on marker-assisted selection for drought tolerance on coffee, the present work had as goals (i) the validation of candidate genes (CG) previously identified by differential gene expression in leaves of tolerant and susceptible clones of Coffea canephora grown in greenhouse under different water conditions and also in leaves of Coffea arabica under field conditions and (ii) the analysis of nucleic polymorphism of some CG. Gene expression experiments were performed in young plants of Iapar59 (drought tolerant) and Rubi (drought sensible) cultivars of Coffea arabica grown in the experimental station of Embrapa Cerrados (Planaltina DF), which is characterized by a regular dry season. Plants were grown under two water treatments: T1 a non limited watering treatment (irrigated during the dry season) and T2 a limited watering treatment (non irrigated during the dry season). Leaf samplings were performed along the two years of the project and used to analyze CG expression by quantitative real-time PCR (qPCR). In parallel, corresponding gene sequences of some CG were also amplified from several coffee (C. arabica and C. canephora) accessions believed to cover these species' genetic diversity for drought tolerance.