Peatlands are critical ecosystems in regulating global carbon cycle and hosting distinctive biodiversity. Chrysophyte stomatocysts, siliceous resting stages of golden-brown algae, are widely distributed in acidic and oligotrophic environments of peatlands. Presently, little knowledge is available on the composition and distribution of stomatocysts in subtropical peatlands. This study investigated the communities of moss-inhabiting stomatocysts in three Sphagnum-dominated peatlands in central China, and their association with environmental variables. Fifty-nine stomatocyst morphotypes with two additional formae were identified according to the International Statospore Working Group guidelines, and stomatocyst assemblages were significantly different among the three peatlands. In addition, these stomatocyst morphotypes were classified into eight morphology-based functional groups according to morphological traits, such as types of collar and ornamentation. Redundancy analyses revealed that stomatocyst assemblages at both morphotype- and functional group-level were significantly correlated with depth to water table, oxidation reduction potential, and morphotype-level composition was further related to electronic conductivity and potassium. Generally, cysts with a complex collar preferred dry hummocks, while large cysts with long spines mainly occurred in wet hollows. This study highlights the usage of chrysophyte stomatocysts as potential bioindicators for environmental changes in these subtropical peatlands, as well as similar peaty environments.