Environmental stress as a consequence of anthropic pressures can affect the physiological condition of animals and cause damage to their DNA. Multiple studies have shown genotoxic effects of different pollutants; however, to our knowledge, the impact of environmental stress on genetic damage has been scarce explored. In some stressful ecosystems, such as seasonally dry tropical forests, the combined effects of anthropogenic activities and ongoing global changes cause increased environmental stresses that could trigger physiological and genetic effects on biodiversity. In this study, we evaluated the changes in the prevalence of genotoxic damage to birds in three states of forest degradation in the Tumbesian Region of Western Ecuador. We used the blood samples of 52 bird species to determine the frequency of micronucleus and nuclear abnormalities in the erythrocytes. Our results showed a significant effect of forest degradation in the proportion of micronucleus and nuclear abnormalities at the community level, localities with higher degradation showed higher levels of abnormalities. However, when analyzing the dominant species, we found contrasting responses. While Amazilis amazilia and Lepidocolaptes souleyetii showed a reduction in the proportion of nuclear abnormalities from the natural to shrub-dominated localities, Troglodytes aedon and Polioptila plumbea showed an increase. We concluded that the degradation process of these tropical forests increases the stress on the bird community generating genotoxic damage to the bird community. Bird responses seem species-specific, which could explain the differences in changes in bird composition reported in other studies.