Aim The Atlantic Forest is a Brazilian biome whose biota plays a fundamental role in the preservation of water quality. Hyphomycetes play an important role in aquatic ecosystems as they can decompose organic matter and, consequently, contribute to nutrient cycling, maintaining aquatic life. The aim of this work was to determine the diversity and composition of the aquatic hyphomycetes community in two areas of Atlantic Forest in the state of Pernambuco (Charles Darwin Ecological Refuge) and Alagoas (Pedra Talhada Biological Reserve), in addition to comparing these communities with the water abiotic factors. Methods For this, four collections of submerged decomposing leaves, for evaluation of the fungi community, and water for measuring the parameters: acidity, alkalinity, chlorides, electrical conductivity, total coliforms, color, BOD, COD, DO, total nitrogen, pH, total solids, sulfates, temperature and turbidity, and calculation of the Water Quality Index (WQI) were carried out. The samplings took place between July/2018 and May/2019, at six points along a stream in each study area. Results Fifty-three taxa were identified, and 1926 occurrences were recorded in 2592 leaf fragments. There was a predominance of Blodgettia aquatica, Blodgettia indica, Flagellospora penicillioides, Flagellospora sp., Mycoleptodiscus disciformis, Triscelophorus monosporus and Xylomyces acerosisporus, with similarity of these and other species between the studied areas. In the rainy season, there was a greater occurrence of aquatic hyphomycetes in both areas; however, the diversity of fungi was greater in the Charles Darwin Refuge. Abiotic factors such as temperature, DO and rainfall influence the occurrence of hyphomycetes, however, no community structure was detected or strongly correlated with the studied abiotic variables. Conclusions The areas presented adequate values for the variables indicative of water quality and high richness of hyphomycetes species, demonstrating the importance of legal protection for the conservation of natural areas.