Soil organic carbon (SOC) fractions play a crucial role in the carbon cycle of alpine wetland ecosystems and regional climate regulation. In the last decades, alpine marshes at Tibetan Plateau have undergone increased degradation. The effects of marsh degradation on soil labile and recalcitrant organic carbon fractions and on SOC stability remain unclear. In this study, we investigated changes in SOC fractions with different biochemical recalcitrance and stability in the marsh ecosystems with various levels of degradation in the Zoige Wetland, Eastern Qinghai-Tibet Plateau. Soil samples of relatively pristine marsh (RPM), lightly degraded marsh (LDM), moderately degraded marsh (MDM), heavily degraded marsh (HDM) and severely degraded marsh (SDM) were collected and analysed using the acid hydrolysis method. Compared with RPM, the concentrations of SOC labile fraction I (non-cellulosic polysaccharides), SOC labile fraction II (cellulose) and recalcitrant organic carbon (ROC) in degraded marshes decreased significantly: 29-97, 38-95 and 32-99%, respectively, except for the LDM. The SOC recalcitrance index (RIc) in the HDM and SDM was significantly lower than that in RPM by 11-35 and 15-47%, respectively; compared with RPM, the stability of organic carbon was significantly lower in the HDM and SDM. Additionally, the marsh degradation increased vertical variation in the concentrations of SOC fractions. The degradation of alpine marshes decreases the capacity for carbon (C) sequestration via decreasing the resistance of SOC to biodegradation, indicating that the alpine marsh degradation may weaken the carbon sink capacity of the Zoige Plateau, thus aggravating the global greenhouse effect. Keywords Zoige. Marsh degradation. Labile organic carbon. Recalcitrant organic carbon. Soil organic carbon stability Highlights • Concentrations of labile and recalcitrant SOC decreased with marsh degradation. • Vertical variation in labile and recalcitrant SOC increased in degraded marshes. • Resistance of SOC to biodegradation decreased after marsh was moderately degraded. • Marsh degradation reduced the capacity of SOC sequestration.