Fluoride is the most phytotoxic atmospheric pollutant. The objective of this study was to evaluate the effects of fluoride emissions by an aluminum smelter on three plant species endemics to Brazil, located at Parque Estadual do Itacolomi (PEI). The monitored species were Byrsonima variabilis (Malpighiaceae), Myrceugenia alpigena (Myrtaceae), and Eremanthus erythropappus (Asteraceae), which were monitored during 9 months using passive biomonitoring at five different locations with different distances from the smelter. The monitored species did not show macroscopic phytotoxicity damage to fluoride; however, they did show microscopic damage. The species closer to the smelter presented more severe anatomic damages, such as rupture of cell walls, protoplast retraction, and trichome alterations. Damaged stomatal ledges, flaking epicuticular wax, and damages to trichomes were observed. M. alpigena showed a higher accumulation of fluoride than the other species at all monitored sites. The test for cell death with Evans Blue was positive for the three studied species. Through biomonitoring in the PEI, we concluded that the emissions from the aluminum smelter affect the native vegetation and that due to the greater accumulation of fluoride and the diversity of microscopic damage in M. alpigena, the use of this species in the monitoring of environments polluted by fluoride is enhanced.