Under the escalating pressures of global warming and ocean acidification, gorgonian coral resources are experiencing continuous degradation. Gorgonian-associated fungal communities, which sensitively reflect coral health status, exhibit close correlations with the ecological conditions of their hosts. However, the diversity and taxonomic composition of these fungal symbionts in the East China Sea remain unreported. To elucidate the taxonomic and community diversity characteristics of gorgonian-associated fungi across different habitats in the Zhongjieshan Islands, 24 gorgonian samples were collected from six stations spanning three habitat types (artificial, mixed natural, and single natural habitats). Fungal isolates were obtained via dilution plate and streak plate methods, followed by molecular identification using ITS and 26S rDNA sequencing to construct phylogenetic trees for taxonomic classification. Functional guilds of the isolated fungi were predicted using the FUNGuild database, and diversity indices (Shannon-Wiener, Margalef, and Pielou) were employed to assess fungal community diversity, richness, and evenness across habitats. A total of 54 fungal strains were isolated and purified, belonging to 31 genera, 25 families, 20 orders, 8 classes, and 2 phyla (Ascomycota and Basidiomycota). Dominant genera included Penicillium (11.11%), Cladosporium (9.26%), and Aspergillus (5.56%). Notably, strains A1, A22, and A53 showed low sequence similarities (92.87%, 90.26%, and 93.04%, respectively) to their closest relatives in the NCBI database, suggesting that 5.56% of isolates represent potential new species. Habitat type significantly influenced fungal community structure: artificial habitats exhibited the highest Shannon-Wiener diversity (2.20) and Margalef richness (2.98), while mixed natural habitats showed the highest Pielou evenness (0.94). In contrast, single natural habitats displayed the lowest diversity metrics. These results demonstrate pronounced habitat specificity and diversity in gorgonian-associated fungal communities within the Zhongjieshan Islands, with artificial habitats likely enhancing fungal colonization through increased environmental complexity. The discovery of potential novel species underscores the region’s untapped fungal resource potential. This study provides foundational data for assessing gorgonian health and formulating targeted ecological restoration strategies, offering critical insights into marine microbial ecology and habitat management.