Water deficits are considered the primary environmental stress in agriculture, and improving the growth and production of plants under this stress is one of the primary goals of breeding and crop management programs. The apple tree is a plant that is negatively affected by water stress. Plants that develop under a water deficit may develop physiological and anatomical strategies to survive or even produce fruits in these environments. In view of the importance of and lack of studies of the leaf anatomy of apple trees in areas with a water deficit that are intended to support genetic improvement programs for this fruit either to introduce cultivars in regions with water deficits or to select potential progenies for future crosses, the aim of this study was to compare the anatomical characteristics of apple leaves from two distinct environments (water deficit and precipitation) under tropical conditions. Twelve fully expanded leaves were collected from seven apple cultivars (Eva, Rainha, Princesa, Julieta, Imperatriz, Baronesa, and Gala Real), which are planted in the experimental orchard at Universidade Federal de Lavras, during water deficit (September) and precipitation (February) seasons. Sixteen anatomical characteristics were evaluated in addition to the anatomical description of the apple leaves. The experimental design was completely randomized in a 7×2 factorial arrangement. The means were analyzed using the Scott-Knott method for grouping means at the 5% level of error probability. Genetic divergence, cultivar clustering and principal component analyses were also performed based on the anatomical characteristics evaluated during the two seasons. The apple leaves had anatomical characteristics that can favor the production of this fruit tree in areas experiencing water deficits within subtropical regions. According to their anatomical characteristics, there was genetic divergence among the apple cultivars studied here. The cultivars Gala Real, Eva, and Baronesa presented anatomical and morphological characteristics that showed adaptation potential in areas with water deficits.