Supplementary and dataset for: <b>A threatened refuge: Northern Red Sea upper mesophotic corals face accelerated warming and species-specific vulnerability</b>

<p dir="ltr">Mesophotic coral ecosystems have gained attention for their potential role as refugia from climate-driven coral bleaching, yet their resilience to prolonged marine heatwaves remains uncertain. Here, we experimentally assessed the thermal tolerance of two Red Sea corals with contrasting depth distributions: the mesophotic specialist <i>Leptoseris glabra</i> and the depth-generalist <i>Acropora squarrosa</i>. Through controlled thermal stress experiments simulating strong to extreme marine heatwave events, we quantified photophysiological, optical, and biochemical responses. Under thermal stress, <i>L. glabra</i> exhibited severe declines in photosynthetic efficiency and energy reserves, coupled by a three-fold increase in tissue reflectance, indicative of extensive symbiont loss. In contrast, mesophotic <i>A. squarrosa</i> maintained stable photophysiology and energy reserves, whereas its shallow conspecific showed marked declines in photosynthetic efficiency, symbiont density, and lipid stores. Skeletal optical analysis revealed that shallow <i>A. squarrosa</i> exhibited higher scattering coefficient and reflectance than its mesophotic counterpart, while <i>L. glabra</i> shared similar optical properties with mesophotic <i>A. squarrosa</i>. These findings suggest that enhanced skeletal light scattering may have exacerbated bleaching in shallow <i>A. squarrosa</i>, whereas reduced light exposure and greater lipid content contributed to mesophotic <i>A. squarrosa’s</i> resilience. Critically, 20-year <i>in situ </i>temperature analysis revealed accelerated warming across intermediate to upper mesophotic depths compared to shallow reefs. This dual threat of species-specific vulnerability combined with accelerated warming at presumed refuge depths, challenges the universality of mesophotic coral ecosystems as thermal refugia and calls for immediate reassessment of depth-based reef conservation frameworks.</p>