Eucalyptus trees are well adapted to various soils and climate environment. However its growth varies strongly according to these factors [1]. Tropical cultivated surfaces are mainly located in water deficient regions during dry season, and there soils are often deficient in potassium (K) [2], an essential nutrient [3] improving plant growth [4] and drought resistance [5]. Sodium (Na) could partially replace it [4, 6]. However, the respective role of K and Na on plant water regulation has still to be established [7]. Here, we present an transcriptomic analysis on Eucalyptus grandis leaves, submitted to normal or reduced rainfalls, and K or Na fertilization. We develop a strategy to analyze gene expression with a multifactor model (fertilization, rainfall regime and interaction of both factors). Then we validate our procedure by analyzing specifically the genes expressed in response to the reduced rainfall regime. Biological processes and genes linked to water deficiency were successfully identified.