Biomarkers analysis serves as an early warning system for the presence of pollutants because their responses appear before irreversible damage to the ecosystem takes place. The genotoxic effects of pollutants may occur at cellular pollutant concentrations that are well below levels that would cause gross cytotoxicity, making this a useful tool to detect early effects of toxic environmental agents. Combining the importance of Brazilian wetlands to the conservation of amphibian biodiversity with the potential negative impacts of irrigated rice fields in the surrounding areas, the aim of the present study was to evaluate genotoxic damage in two amphibian species, Pseudis minuta, and Leptodactylus gr latrans, from the southern Brazilian wetlands. Adult specimens from both Anuran species were captured from preserved (Taim Ecological Station=TAIM) and non-preserved (Senandes) wetlands. Nuclear abnormalities were quantified in erythrocytes, and the results were compared using the Mann–Whitney U test. There was a higher incidence of micronucleated erythrocytes in P. minuta, and of notched nuclei in L. gr latrans that were collected in TAIM when compared to those that were collected in Senandes, despite the fact that TAIM is a conservation unit. These findings indicate that Anurans are coping with genotoxic substances in their habitats, and underscore the need to implement monitoring programs in TAIM to determine which compounds or mixtures might be causing cell damage and to investigate the effects of such compounds on other anuran species and animal groups.