[Objective] to investigate the diversity of marine fungi producing extracellular protease isolated from the intertidal zone of Naozhou Island in the South China Sea. [Methods] The samples of both seawater and sediment were collected from the intertidal zone of Naozhou Island in South China Sea, and used to investigate the diversity of the fungi producing extracellular proteases by culture-dependent method, protease producer plate assay, and a phylogenetic analysis based on the sequences containing internal transcribed spacer 1, 5.8S rRNA gene and internal transcribed spacer 2 (ITS1-5.8S-ITS2). [Results] A total of 198 isolates of fungi were isolated, purified and collected from the samples on the plates of Potato dextrose agar (PDA) medium prepared with 50% seawater. Amongst these isolates, 178 strains were identified successfully by PCR amplification, sequencing, BLAST and phylogenetic analysis of the ITS1-5.8S-ITS2 sequences. All these sequences showed ≥98% identity with the existing relative ITS1-5.8S-ITS2 sequences in the GenBank database, except 10 strains showed the identity <97% with their closest match suggesting their possibility of being novel species. These 178 strains represented 66 species, belonging to 45 genera of 27 families in 16 orders, 6 classes, spreading in two phyla, Ascomycota and Basidiomycota. The predominant genus was Penicillium, which takes a great proportion of 28.70%, followed by Aspergillus, which takes a proportion of 11.24%. There were 83 identified strains showed clear zone around their colonies on the PDA plates supplemented with skim milk indicating they could produce extracellular proteases. [Conclusion] A total of 178 strains of fungi were isolated and identified from the intertidal zone of Naozhou Island in the South China Sea. Amongst these strains, 10 strains would be novel specie Candidates, and 83 strains could produce extracellular proteases.