Eucalypt plantations in Brazil have expanded towards regions with long dry periods and low fertility soils. During the dry season plants under water stress show young leaves with interveinal chlorosis and curled and branches tip dye back induced by boron (B) deficiency. Symptom intensity varies among eucalypt genotype signaling to differential drought tolerance among genetic materials. Previous experiences have shown that supplying B just before water stress allows satisfactory plant growth and stimulate the expression of genes related to cell wall formation and B transport in the plants, particularly in roots of tolerant genotypes. This research aimed to evaluate B effect on differential transcription of genes related to cell wall synthesis and alterations (PME3 and GTP8) and B uptake and transport (BOR cl6871, BOR5, BOR2) in eucalypt clonal seedlings under water stress. Twenty-four plastic trays, containing 10 L of a complete nutrient solution, received four eucalypt seedlings each. Boron was supplied as 11 B (99 atom %) in the concentration of a 5 µmol L-1. After thirty days in the nutrient solution the seedlings were split into two groups. In sixteen trays seedlings were grown in the nutrient solution, without B, and in eight they were grown with 15 µmol L-1 de 11B (99 atom %) in the solution for 25 days. Finished this period, increased doses of polyethyleneglycol (PEG) 6000 (100, 200, 250 e 360 g/L) were added every five days to raise gradually the nutrient solution tension to 0,15; 0,65; 1,00 e 1,5 MPa, according to the treatments. After PEG addition, B was removed from the nutrient solutions where it was still present. Therefore, four treatments were generated: a) plants under no- water stress and no B in the nutrient solution (SS –B); b) plants under no- water stress and with B in the nutrient solution (SS +B); c) plants under water stress and no B in the nutrient solution (CS –B); d) plants under water stress and with B in the nutrient solution (CS +B). Two additional treatments consisted of plants under water stress and no B in the nutrient solution but: i) foliar 10 10 B (99 atom %) application to a mature leaf (CS BFM), and ii) foliar B (99 atom %) application to a young leaf (CS BFJ). Seedling biomass production and leaf water potential were negatively affected by water stress and no B application. Gene expression was augmented in plants submitted to water stress but supplied with B, except for BOR2. Boron application to mature leaves of seedlings under water stress mitigated the negative effects of the water stress by increasing root growth and drought tolerance.