Medicinal plants have been used in primary healthcare since the earliest days of humankind. Turnera subulata and Spondias mombin × Spondias tuberosa are widely used in the Brazilian Northeast to treat several diseases. The aim of this study was to evaluate the genotoxic effects of the leaf extracts of these species by the somatic mutation and recombination test in the somatic cells of Drosophila melanogaster wings. The experiments were performed using standard and high-bioactivation cross and three concentrations of the test substance [aqueous extract (AET and AES) at 5.0, 10.0, and 20.0 mg/mL and ethanolic extract (EET and EES) and ethyl acetate fraction (EAFT and EAFS) at 0.625, 1.25, and 2.5 mg/mL]. Results indicated that the extracts and fractions induced spontaneous frequencies of mutant spots in both D. melanogaster crosses. Nevertheless, the highest concentrations of the tested plant chemical agents were responsible for the statistically significant genotypic effect. T. subulata and S. mombin × S. tuberosa displayed genotoxic effect under the experimental conditions. The results from this study are crucial as they indicated the deleterious and side effects, considering the indiscriminate use of the extracts of these plants for disease treatment.