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Background and aimsMicrobial communities are the primary drivers of organic matter decomposition in peatlands. However, limited knowledge is available regarding depth-dependent microbial community structure and function in East Asian peatlands, using cultivation independent approaches.MethodsWe investigated the vertical stratification of prokaryote and fungal communities in a moderately rich fen in northeast China (Hani) and a rich fen in southwest China (Riganqiao).ResultsFungal and prokaryotic operational taxonomic unit (OTU) composition exhibited strong site and/or depth responses. Prokaryotic OTUs exhibited the greatest alpha diversity at the mesotelm hot spot', whereas the predicted metagenomic metabolic functions did not align with the pattern of prokaryote alpha diversity. The large cover of shrubs contributed to a greater relative abundance of ericoid- and ecto-mycorrhizal fungi at Hani, whereas Riganqiao showed more arbuscular mycorrhizal fungi. Soil pH and water table depth were among the predominant abiotic factors associated with microbial community composition.ConclusionsProjected shifts in hydrology and/or vegetation with global change may cause substantial impacts on peatland microorganisms and thus the associated biogeochemistry. It is critical to better understand the mechanism of the discrepancy between microbial community structure and the functions at the mesotelm hot spot' when evaluating the ecosystem functions in peatlands.