Native plants from the Brazilian savanna (the Cerrado) are exposed to agrochemicals widely used in the crops around them. However, there are few studies on the toxicity of herbicides on the vegetation of this biome. Thus, the objective of this study was to identify and establish morphological and physiological indicators of glyphosate effects on two native Cerrado plants. Independent experiments were carried out for the species Pouteria torta and Alibertia edulis , exposing them to four glyphosate doses (0, 200, 400, and 800 g a.e. ha −1 ). The photosynthetic process and the morphoanatomy in developing leaf (F1) and full-expanded leaf (F3), at different days after herbicide application (DAA) were evaluated. Physiological indicators of glyphosate toxicity in P. torta , such as decreases in photosynthetic rate, in chlorophylls, and in the efficiency of photosystem II were identified. Increments of carotenoids and heat dissipation (NPQ) were common responses to glyphosate in both plants. Reduction in photochemical efficiency in A. edulis was more pronounced in older leaves. Multivariate analysis confirmed the physiological data and the contrasting response of plants to the herbicide. The damages on the foliar surface in P. torta are anatomical indicators of glyphosate toxicity. The susceptibility of P. torta makes it a phyto-indicator for the passive biomonitoring of the glyphosate effects on Cerrado vegetation. There were no changes in the micromorphology of the leaf surface in A. edulis . This plant showed tolerance to the glyphosate through morphological barriers in leaves, which reduced the absorption of the herbicide.