Egypt is considered as a white spot for fungal biodiversity thus, this study used ITS sequencing, and routine identification to analyze the fungal communities within different marine sources (sediments, water, algae, and wood) from the Egyptian Mediterranean Sea at Alexandria coastline, which helped to uncover fungal diversity and distribution pattern. Two hundred fifty-two marine fungal isolates were isolated from twenty-five sea sediment, seven water, eight algae, and eight wood samples, which were collected seasonally through sex trips during the year 2017/2018 from the Egyptian Mediterranean Sea, Alexandria, Egypt. In the present study, sediment samples contained the highest diversity of fungi, and the most dominant phylum was the Ascomycota (90.8% OTUs) followed by the Basidiomycota (6.7% OTUs). A small proportion of the OTUs was assigned to the Mucoromycota. Some available indices had been successfully followed during this study for estimating the fungal biodiversity, and these indices proved their effectiveness.