Here we provide ITS2 sequences of Symbiodiniaceae that were sequenced from juveniles of the soft coral Rhytisma fulvum from shallow and mesophotic depths In Eilat (northern Red Sea). The samples were paired-end sequenced (2 x 250 bp) on the NovaSeq 6000 platform at the Novogene Sequencing Centre. We used the Sym-Var primers (Hume et al. 2018).