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Abstract Essential to life on Earth, assessment of marine photosynthesis is of paramount importance. Photosynthesis occurs in spatially discrete microscopic entities at various levels of biological organization, from subcellular chloroplasts to symbiotic microalgae and macroalgae, and is influenced by the surrounding conditions.As such, in situ photosynthetic efficiency mapping on appropriate scales holds great promise for learning about these processes.To achieve this goal, we designed, fabricated, and tested an underwater microscope that incorporates standard colour, epifluorescence, and variable chlorophyllafluorescence imaging with nearly micron spatial resolution that resolves the structure and photosynthetic efficiency of benthic organisms.Our results highlight coral observations with high‐resolution photosynthetic spatial variability and detailed morphology. Our imaging system therefore enables research never before possible on the health and physiology of benthic aquatic organisms in situ, placing it in the context of their physical and biological environment.