Abstract: Aquatic plants are the main primary producers in shallow lake, and their decomposition and mineralization have significant effects on the nutrient cycle in lake ecosystems. Fungi are one of the major decomposers in natural environments, but little is known about the composition and functions of fungal community during the decomposition of various aquatic plant litters. In this paper, various types of aquatic plant residues were separately added into undisturbed lake sediments and their upper water to study the characteristics of fungal community structure during the decomposition of these residues, based on the selection of suitable primers that can specifically amplify fungal 18S rRNA gene and on the construction of clone libraries and sequencing. The results showed that the primer pairs nu-SSU-0817/nu-SSU-1536 and nu-SSU-0817/nu-SSU-1196 were suitable to amplify the fungal 18S rRNA gene. Basidiomycota was the most common fungal taxa in water column, and Chytridiomycota was the most common one in surface sediments. Statistical analysis showed that there existed obvious differences in the fungal community structure in water column and surface sediments. This study would give further insight into the functions and niche differentiation of fungi during the decomposition of aquatic plant litters.