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Aquatic hyphomycetes are a group of asexual fungi specialized in the decomposition of organic matter and nutrient cycling in aquatic ecosystems. The study of the diversity of aquatic hyphomycetes is of great ecological importance, since these fungi are indicators of the quality of aquatic ecosystems. In this research, the diversity of aquatic hyphomycetes was analyzed from samples of foam and submerged leaf litter with evidence of decomposition, collected from the upper, middle and lower course of Caimito river, using the Shannon-Wiener index to evaluate diversity. A total of 51 morphospecies were identified, of which 43 were classified at the species level, distributed in 35 genera. The distribution within the Caimito river course was 27 morphospecies in the upper course, 26 in the middle course and 25 in the lower course. The total diversity index was 2.65, which indicates a medium diversity and suggests a relative stability in the aquatic ecosystem, although possibly affected by anthropogenic activities.