Mouriri elliptica (Mart.) is a genetic resource of the Cerrado domain, which has potential for food and medicinal use. A few studies have been performed on its in vitro propagation, and no studies have examined dissimilarities between plants of this species when cultivated in situ or in vitro. Therefore, the objective of the present study was to identify in vitro cultivation conditions that permit the formation of plantlets with leaf anatomical features that are less dissimilar to those of plants grown in situ. Thus, an anatomical study of the leaves was conducted to investigate the adaxial epidermis thickness, abaxial epidermis thickness, chlorenchyma thickness, stomatal crypt depth, stomatal crypt density, and leaf surface stomatal crypt aperture area. The distance between phenotypes was determined based on micromorphometric data, and unweighted pair group mean arithmetic clustering was performed. Four different groups were tested, and cultivation with sucrose and 50 and 75 μmol⋅m⋅s irradiance was found to promote plantlet development and maximize similarity to plants cultivated in situ. The most important anatomical parameters in this study were the stomatal crypt aperture area and the crypt density. This study is of importance for the anatomical characterization of M. elliptica (Mart.) leaves, as it identifies plasticity as a function of in vitro culture conditions.