In light of global climate change, identifying critical marine habitats and conserving them is essential. Marine conservation planning recommends designating cooler habitats as marine protected areas. The ‘deep-reef refugia’ hypothesis suggests that deeper, suitable habitats may allow species to undergo the evolutionary changes necessary to adapt to the growing environmental threats they face. This hypothesis has rarely been tested outside tropical ecosystems, where it has been fully or partially rejected. This study, using a systematic approach, is the first to evaluate this hypothesis regarding fish communities in the East Mediterranean Sea (EMS), which is warming at an unprecedented rate. Fish were surveyed twice a year from 2015 to 2022 across three rocky habitats: shallow (10 m depth, 23% ± 11 of 1 m Photosynthetically Active Radiation, PAR), upper mesophotic (25 m depth; 8% ± 4 of 1 m PAR), and lower mesophotic (45 m depth; 3% ± 2 of 1 m PAR), using closed-circuit rebreather systems. Data collected from 357 belt transects indicate that: 1) species and functional diversity of the shallow habitat are encompassed within those of the deeper habitats; 2) gamma diversity is greater in the upper mesophotic community; 3) alpha diversity in the upper mesophotic is higher compared to shallow depths; 4) beta diversity increases with depth. Unlike most findings on tropical coral ecosystems, our results suggest that a fish community is currently thriving in the rapidly warming Eastern Mediterranean Sea (EMS) at upper mesophotic depths. This community appears to act as a climate change refuge for a less diverse, shallower community. The unique position of the EMS as a transitional marine environment emphasizes its potential role as an early indicator of changes in fish depth distributions that could globally impact subtropical ecosystems.