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Abstract Ten coral samples were collected from El-Ein El-Sokhna, Red Sea, Egypt. They were identified as Acropora humilis, Acropora cervicornis, Galaxea fascicularis, Favia speciosa, Cladocora arbuscula, Isophyllastrea rigida, Stylophora pistillata, Pterogorgia guadalupensis, Pavona clavus and Porites astreoides. The highest fungal count and species diversity isolated from hard corals were achieved using the blender technique and a medium of Dextrose Yeast Extract agar (DYA). On the other hand, the dilution technique and a medium of Rose Bengal agar (RBA) achieved the highest count and diversity of endosymbionts isolated from soft corals. A total of 137 fungal isolates constituting 18 species were isolated from the aforementioned ten coral samples of which 80 isolates came from hard coral samples and 57 isolates came from soft coral samples.The hard coral sample Acropora humilis exhibited the highest fungal diversity among hard corals (6 species) while the soft coral sample Isophyllastrea rigida recorded the highest fungal diversity among soft corals (7 species). Images of the coral samples obtained by Scanning Electron Microscope (SEM) showed the presence of spores and mycelia of endosymbiotic fungal species spread between and attached closely to the coral skeletal pores and cavities. The biological activity of the prevalent active endosymbionts revealed that they all exhibited antimicrobial and antioxidant activities. Aspergillus ochraceopetaliformis and Byssochlamys spectabilis proved to be the most biologically active species. Those fungal species also showed cytotoxicity against a human liver carcinoma (HEPG-2) cell line. Molecular identification using 18S rDNA, PCR, DNA sequencing and phylogenetic analysis indicated that those coral fungi are A.ochraceopetaliformis strain CBS123.55 with accession number MH857406 and B.spectabilis strain PAEC with accession number KR909186 |