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Coral reef ecology has advanced in many fields, but disease patterns across depth gradients remain unclear. By comparing the prevalence and extent of bleaching and diseases in 160 colonies of Siderastrea stellata between shallow and mesophotic reefs, we observed that prevalence was high (75%) regardless of depth, but the extent was about two times greater in mesophotic than shallow reefs (14.4% vs. 6.6% of colony area, respectively). Across the shallow reefs, where S. stellata co-occurred with Montastraea cavernosa, M. cavernosa showed lower prevalence (27% of 30 colonies) and extent (1.8% of colony area) compared to S. stellata. Besides bleaching, five coral diseases afflicted S. stellata and two affected M. cavernosa. Because diseases are spread over the entire gradient of depth, any attempt of managing the diseases should consider both shallow and deep reefs to be effective.