The chemical quality of soil carbon (C) inputs is a major factor controlling litter decomposition and soil C dynamics. Mycorrhizal fungi constitute one of the dominant pools of soil microbial C, while their litter quality is understood poorly, leading to the major uncertainties in estimating soil C dynamics. For the first time, we examined chemical recalcitrance of arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) fungal species using fungal samples obtained from in vitro cultivation. We show that the chemical composition of AM and EM fungal mycelium differs significantly: EM fungi have higher concentrations of labile (water-soluble, ethanol-soluble) and recalcitrant (non-extractable) chemical components, while AM fungi have higher concentrations of acid-hydrolysable components. Our results imply that differences in chemical decomposability traits among mycorrhizal fungal guilds represent a critically important driver of the soil C cycle, which could be as vital as is recognized for differences among aboveground plant litter.