Fungal biomass and guild dominance jointly govern soil organic carbon pools in alpine treeline ecosystems

• Fungal biomass is controlled more by treeline tree species than by elevation. • Fungal biomass is tightly coupled with soil total carbon (∼33–39% explained). • In the larch treeline ecotone, fungal biomass explains 18.2% of SOC content. • Higher ectomycorrhizal fungal dominance enhances SOC persistence. Climate warming threatens soil organic carbon (SOC) storage in alpine ecosystems, where soil fungi play an important role in promoting belowground carbon sequestration. We quantified total and guild-specific fungal biomass along two alpine treeline ecotones in Baima Snow Mountain, southwestern China. Rhizosphere soils were sampled from two dominant treeline species— Abies georgei (AG, 3768–4385 m) and Larix potaninii (LP, 4036–4534 m). High-throughput sequencing combined with ergosterol analysis was used to characterize fungal biomass, functional-guild composition, and their relationships with SOC pools. Total fungal biomass showed no consistent elevational pattern but varied strongly between tree species. In the LP ecotone, fungal biomass was the strongest predictor of SOC content, explaining 18.2% of its variation. Across both ecotones, SOC persistence increased with the relative dominance of ectomycorrhizal fungi, quantified as the ratio of ectomycorrhizal to plant-pathogenic or saprotrophic fungal biomass. Our results demonstrate that treeline tree species regulate alpine SOC storage by shaping soil fungal biomass and functional-guild structure. Greater fungal biomass promotes SOC accumulation, whereas ectomycorrhizal dominance enhances SOC persistence—highlighting a key microbiological pathway regulating belowground carbon sequestration in alpine environments.