Corals form a symbiotic relationship with photosynthetic zooxanthellae from the genus Symbiodinium; the breakdown of this symbiosis results in the phenomenon known as coral bleaching. This relationship is especially vulnerable to high temperature stress, although corals may survive if they have resistant types of symbionts, or switch their community composition towards them. To assess the variation of the symbiont community in different environmental conditions, I recorded the temperature and collected samples from six scleractinian coral species and one calcifying hydrozoan, in two inshore, two mid-shelf, and two offshore reefs at 1, 15, and 30m depth, analyzing Symbiodinium diversity using Next Generation Sequencing with the SymPortal profile typing approach. The temperature was very similar for all points in winter, when coral samples were collected, but variation between points increased until a maximum at summer, with the shallower parts of the inshore reefs showing higher temperatures and the points at 30m depth showing the lowest. The Symbiodinium composition was more similar between samples of the same host species than among samples of the same reefs or depths. Coral species from the Pocilloporidae family and Millepora dichotoma showed specific association with different profile types, specifically, intragenomic variants of Symbiodinium type A1, which appears to be dominant in the Red Sea although it has not been reported for these species in other regions. The other species showed specific associations with types previously reported in other regions, mostly from clade C and D, although also having different types and intragenomic variants. For most cases, certain profile types, which can reflect different species or populations, appeared to be dominant in particular environmental conditions, following a distribution related with depth, reef type, or both. In conclusion, this study showed that the Symbiodinium composition depends more on the host species than on the environmental conditions, and within each species the adaptation to environmental gradients can rely on tolerant symbiont species or populations characteristic of the Red Sea, or association with different types and clades that are common also in other regions.