Drought stress promotes biochemical and physiological alterations in plant metabolism that limit growth and yield. This study investigated the accumulation of γ-aminobutyric acid (GABA) in plant tissue, the stomatal conductance (gs) and changes in leaf anatomy in Eucalyptus following drought stress situation. In this study, eight Eucalyptus clones were evaluated under normal water supply (control) and drought stress conditions (stress). For the control treatment, plants were irrigated every day with an automated system until the soil was saturated, and for the stress treatment, drought stress was imposed by non-irrigation of plants, and pots were covered using plastic sheeting to avoid rainfall and humidity. This study has shown that: (1) all clones decreased gs with increasing vapor pressure deficit (D) in both treatments. All plastics and drought-tolerant clones (except GG) presented lower stomatal sensitivity to D under stress conditions than drought-sensitive clones; (2) GABA concentrations increased fast after drought stress, but we could not find correlation with these changes and resistance to water stress; and (3) all clones increased the number of stomata and reduced leaf thickness after water stress. The finding is that GABA is a fast stress-signaling molecule in Eucalyptus, but the response of gs to D is a best physiological variable to differentiate drought-tolerant and drought-sensitive Eucalyptus clones.