The Gulf of Aqaba and Northern Red Sea are among the least explored basins of the Indo-Pacific region. There, while the shallow Red Sea coastal benthic habitats have been extensively characterised and their zonation in relation to environmental factors described, mesophotic and deep-sea habitats remain comparatively poorly characterised. These habitats develop in a water column that, unlike in most of the global ocean, remains warm (~21 °C) and hypersaline (~40.6) below the pycnocline. In this context, we present the first regional assessment of benthic habitat zonation from the mesophotic to the deep zone (70–700 m) along the Saudi Arabian margin of the Gulf of Aqaba and Northern Red Sea. Using high-resolution multibeam bathymetry, CTD profiles, and over 135 hours of high-definition footage from underwater vehicles, we developed a hierarchical habitat classification, integrating physiography, substrate, terrain analysis, and visually identified biota. Fourteen distinct benthic habitats were identified, including crustose coralline algae- and rariphotic coral-dominated bioconstructions, octocoral-dominated assemblages and deep scleractinian coral frameworks. Oceanographic parameters (temperature, salinity, oxygen concentration) and seafloor morphology were both associated with habitat spatial distribution across the two basins. Multivariate analyses revealed a consistent vertical zonation, with three ecological breaks at approximately 100, 120, and 160–180 m depth, delineating four successive zones from the lower mesophotic to the deep azooxanthellate assemblages. This work fills a major knowledge gap for the Red Sea's deep-water ecosystems, providing a critical baseline to support future monitoring, conservation, and management strategies in a rapidly developing region.