Interaction between marine macrophytes and microorganisms plays a crucial role in maintaining the health of marine ecosystems and supporting biogeochemical cycles. However, there have been few studies on the microbiome in macroalgal blooms, and compared to bacteria, fungal communities remain relatively unexplored. In the present study, we conducted monthly collections of Ulva ohnoi, a causal agent of macroalgal blooms in Jeju, and its nearby water during the outbreak and decline of algal blooms. The dynamics of fungal communities of the internal and external part of algal tissues during the outbreak and decline of algal blooms were determined using eDNA metabarcoding, and compared with those present in the surrounding water. Our findings revealed that the relative composition of fungal communities, primarily consisting of Alternaria, Cladosporium, Fusarium, Golovinomyces, Mycosphaerella, and Penicillium in Ascomycota, as well as Athelia in Basidiomycota, underwent significant shifts in response to algal bloom events across all habitats. However, the fungal structure and diversity within the internal and external portions of algal tissues exhibited marked contrasts when compared to those in the surrounding water. Our study highlights the significant heterogeneity of the fungal microbiome (mycobiome) by the algal bloom. This finding suggests further research on the functional importance of fungi related to the marine environmental change and biogeochemical cycling.