Symbiotic associations, widespread in terrestrial and marine ecosystems, are of considerable ecological importance. Many tropical coral species are holobionts, formed by the obligate association between a cnidarian host and endosymbiotic dinoflagellates of the family Symbiodiniaceae. The latter are abundant on coral reefs from very shallow water down to the upper mesophotic zone (30-70 meters).</p><p>Here, we used high-throughput sequencing of the ITS2 region to characterize the dominant and the rare Symbiodiniaceae lineages found in several depth-generalist species across the depth gradient. ITS2 region of Symbiodiniaceae rRNA was amplified using Symbiodiniaceae-specific primers and pooled indexed libraries and sequenced in HyLabs, Israel on aIllumina MiSeq