ABSTRACT Background: Many fringing coral reefs are exposed to anthropogenically derived eutrophication. In scleractinian corals, this type of pollution induces alterations in complex physiological functions, ranging from changes in growth rates and reproductive effort to reduction in immunity, factors that can have dire effects on coral biodiversity. The complexity of effects of eutrophication on coral physiology can be confusing and additional tools are needed to clarify these effects. Aims: Using cellular diagnostics, we compare the physiological status of colonies of the coral Stylophora pistillata growing in a eutrophic environment with the status of reference colonies growing nearby in minimally polluted water. We evaluate the usefulness of the cellular diagnostics for discerning causality by comparing the results with previously observed differences in physiological parameters. Location: Northern Gulf of Aqaba, Israel. The reference colonies grew near the Egyptian border at Taba. The colonies in eutrophic water grew 11 km to the north near net-pen fish-farms. All sites were on a sandy bottom, 19 m deep. Methods: We used biomarkers of general metabolic condition, protein synthesis and maturation, and of oxidative stress and response to assess and compare the cellular physiological status of coral colonies and their algal symbionts from the two sites. Results: Cellular diagnostics showed either site-specific or treatment-specific differences or both. Markers of protein synthesis and maturation showed both site-and treatment-specific differences. Host and zooxanthella Hsp60, and zooxanthella Cu/ZnSOD, were elevated in transplanted colonies compared with native and reference colonies. Differences in levels of host Hsp90 were site specific and were significantly higher in fish-farm colonies than in reference colonies. Despite this, no associated elevation in ubiquitin was apparent in these colonies. The higher concentrations of mitochondrial aconitase in fish-farm colonies corroborate the increased growth rate previously observed in these colonies. Concentrations of markers of oxidative condition were generally lower in fish-farm colonies than in the reference colonies, reflecting lower photosynthesis due to less light at the site. Levels of xenobiotic response markers showed that corals in the fish-farm environment were not detoxifying substances usin