This study addresses the understanding of fungal diversity and their bioremediation roles in an integrated aquaculture wastewater bioremediation system, an area less explored compared to bacteria, viruses, and protozoa. Despite the rapid advancement and affordability of molecular tools, insights into fungal communities remain vague, and interpreting environmental studies in an ecologically meaningful manner continues to pose challenges. To bridge this knowledge gap, we developed an integrated aquaculture wastewater bioremediation system, incorporating photosynthetic bacteria, and utilizing internal transcribed spacer (ITS) sequencing to analyze fungal community composition. Our findings indicate that the fungal community in aquaculture wastewater is predominantly composed of the phyla Ascomycota and Chytridiomycota, with dominant genera including , , and . FUNGuild, a user-friendly trait and character database operating at the genus level, facilitated the ecological interpretation of fungal functional groups. The analysis revealed significant negative correlations between nutrient levels (COD, NH-N, NO-N, NO-N, and PO-P) and specific fungal functional groups, including epiphytes, animal pathogens, dung saprotrophs, plant pathogens, and ectomycorrhizal fungi. The removal rate for the COD, NH-N, NO-N, NO-N, and PO-P were 71.42, 91.37, 88.80, 87.20, and 91.72% respectively. This study highlights the potential role of fungal communities in bioremediation processes and provides a framework for further ecological interpretation in aquaculture wastewater treatment systems.