The use of fish species uses as bioindicators is an important environmental monitoring tool. Histological biomarkers are adopted to assess the health conditions of different organisms and to indicate an environmental hazard. Histology can be applied as an effective method to analyze the effects of pollutants and other stressors. Accordingly, histological changes in the gill epithelium were analyzed to assess the adoption of fish species Menticirrhus americanus (Linnaeus, 1758) and Micropogonias furnieri (Desmarest, 1823) as a bioindicator to measure environmental quality in Paraty and Sepetiba bays, in Rio de Janeiro. A random sample of 58 fish was collected from the assessed bays. We found Paraty Bay to be in good conservation condition, whereas Sepetiba Bay is contaminated. The fish species collected from Sepetiba Bay showed lesions such as epithelial lifting, aneurysm, and necrosis in the gills; thus, it was possible to suggest that histological biomarkers be used bioindicators to measure the environmental impact in these bays.