We evaluated the genotoxic potential of surface water bodies in an area impacted by agrochemicals, in the Ibicoara-Mucugê agropole, Bahia and those within protected areas in Chapada Diamantina, Bahia, Brazil, using the micronucleus test as a biomarker in tadpole species native neotropicals. Our hypothesis is that the closer to agricultural farms, the more affected by mutagenic and genotoxic substances will be the environment and resident organisms. The micronucleus frequencies were determined in tadpoles of 11 species collected in 11 surface water bodies in coffee, corn, vegetable, and pumpkin plantations, as well as in adjacent sites within a protection area. Tadpoles of seven species found in agricultural sites exhibited higher frequencies of micronuclei compared to the six species from the protected locations. The species Bokermannohyla oxente and Leptodactylus latrans collected in agricultural areas exhibited the highest frequencies of micronucleated erythrocytes compared to the populations from the protected areas (p <0.05). Our results indicate that compounds present in surface water bodies in agricultural areas of the Ibicoara-Mucugê farm have genotoxic effects on anurans, showing the stress responses caused by agricultural activities associated with the use of complex mixtures of pesticides. Thus, anurans are excellent sentinel species in environmental monitoring, previously indicating the effect of xenobiotics on the environment.