The depth at which Mesophotic Coral Ecosystems (MCEs) are found (30 to 100 m) acts as a buffer against extreme temperatures and storms. Therefore MCEs may provide a refuge and replenishment source for degraded shallow reefs as stated by the Deep Reef Refugia Hypothesis (DRRH). The tridimensional structure of scleractinian corals provides ecological niches colonized by symbiotic organisms that contribute to increase the coral-guild resistance. While the importance of endo- and exo-symbiotic communities is well recognized for shallow corals, it remains largely unexplored in MCEs. In this context, we compared symbiotic communities from upper MCEs (40 m depth) versus shallower reefs of Okinawa focusing on communities naturally associated to pocilloporid and acroporid corals. In addition, we performed a transplantation experiment of the pocilloporid coral Seriatopora hystrix to understand the dynamic of endo- and exo- symbiotic communities at different depths. Our results highlighted an overlapping biodiversity between the two depths that will be discussed within the frame of the DRRH.