Stony corals are long-lived, calcifying cnidarians that provide critical records of past coastal environmental conditions. In this study, we analyze sub-fossil Cladocora sp. colonies excavated from the ancient port of Akko, Israel, dated to the Hellenistic period (~335–94 BCE), alongside modern Cladocora caespitosa from Haifa Bay. The sub-fossil corals, preserved within archaeological strata, offer insights into past seawater conditions, anthropogenic influences, and harbor dynamics. We employ micromorphology, stable isotope analysis, and ancient and modern DNA sequencing to assess species identity, colony growth form, and environmental conditions experienced by the corals. Comparisons between sub-fossil and modern specimens suggest that Hellenistic Akko corals grew in a high-light, cooler-water, and high-energy environment, potentially with exposure to terrestrial waste. The exceptional preservation of these colonies indicates a rapid burial event, possibly linked to ancient harbor activities or extreme sedimentation. Our results also demonstrate the utility of scleractinian corals as paleoenvironmental archives, integrating biological and geochemical proxies to reconstruct past marine conditions. By linking archaeological and ecological records, we can provide a more comprehensive view of human-environment interactions across time. This multidisciplinary approach, covering physical and natural sciences as well as social science, enhances our understanding of historical coastal dynamics and informs interpretations of ancient harbor use, climate variability, and anthropogenic impacts.

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