Symbiont-bearing foraminiferal assemblages from reef environments have proven useful as ecological indicators for water quality. Studies with other organisms have utilized cellular biomarkers to elucidate mechanisms of stress response. Our goal was to combine these approaches, focusing on populations of the symbiont-bearing foraminifer Amphistegina lessonii from Fernando de Noronha Archipelago (northeastern Brazil). Reef-rubble samples containing A. lessonii were collected at five sampling sites on the leeward side of the main island. Three sites were located inside and two outside the Fernando de Noronha National Marine Park (FNNMP) area. Foraminifers were evaluated regarding their density, degree of bleaching, antioxidant capacity against peroxyl radicals (ACAP), lipid peroxidation (LPO), protein carbonylation (PC), and concentrations of metallothionein-like proteins (MTs). Densities of A. lessonii were lower at sites located outside the FNNMP, compared with those inside the FNNMP, where the maximum average was 159±29 individuals/100 cm2. In individuals from sites located outside FNNMP, bleaching frequency reached 25%, though <2%; at FNNMP sites (<1.8%;). ACAP was higher (two-fold) in individuals collected at the FNNMP sites, which showed lower LPO and PC levels. MTs concentration did not differ significantly among sites. Zinc, copper, and lead concentrations were very high at stations located outside FNNMP. Dissolved organic carbon concentration was high at all sampling sites. Redundancy analysis revealed a strong correlation between biomarkers and water quality among sampling sites. These results show that the biomarker approach would be effective in identifying impacted areas and underlying causes, providing a reliable diagnostic for environment health.