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There is a growing concern that the on-going and future global warming would change the C cycling in northern peatland ecosystems. The peatlands in the Sanjiang plain could be more vulnerable to global warming because they are mainly located at the most southern regions of northern peatlands. Compared with bacteria, fungi are often overlooked; even they also play important roles on the substance circulation in the peatland ecosystems. Accordingly, it is imperative that we deepen our understanding on fungal community structure and diversity in the peatlands. In this study, the relative abundance, distribution, and composition of fungal communities in three different minerotrophic fens distributed in the Sanjiang Plain, was investigated by next-generation sequencing. A total of 533,323 fungal ITS sequences were obtained and these sequences were classified into at least 6 phyla, 21 classes, more than 60 orders and over 200 genera, suggesting a rich fungal community in this ecosystem. The dominated taxa were confirmed to be frequently detected in other northern peatland ecosystems. In comparison with pH, the TC, TN, C/N ratio, and bulk density were determined to be more important environmental parameters shaping fungal community structure. Additionally, for the first time, we found the distribution patterns of several abundant fungal taxa were closely related to the soil age and C accumulation rate.