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Soil organic carbon (SOC) decomposition can potentially feedback to climate change. However, the biotic, abiotic and inherent factors controlling the stability of soil carbon, and changes in these factors with soil depth, remain poorly understood. In this study, we combined a number of complementary methods to quantify the biological, thermal, chemical, molecular and isotopic indices of soil organic matter (SOM) stability along the soil profile (0-70 cm) in two contrasting alpine ecosystems (meadow and shrubland) on the Tibetan Plateau. Firstly, we conducted an aerobic lab-incubation experiment on root-free, sieved soils. The number of days to respire 5% of initial SOC, a biological index of SOM stability, decreased with soil depth. Moreover, the temperature at which half of SOM mass loss (TG-T50), a thermal index of SOM stability, increased with soil depth. Additionally, hot-water extractable organic carbon (HWEOC) per gram SOC, a chemical index of SOM stability, showed weak (meadow) and little (shrubland) declining trend with depth. Further, we used Fourier-transform infrared spectroscopy (FTIR) and nuclear magnetic resonance (NMR) spectroscopy to characterize the molecular composition of SOM. The index of recalcitrance of FTIR spectra and the combined index of aliphaticity and aromaticity of NMR spectra both increased with depth, suggesting that the molecular composition of SOM was more complex with increasing depth. Finally, the isotopic values of SOM (C-13 and N-15) and the C-14-based SOC turnover time both increased with depth, indicating that the isotopic indices of SOM stability also increased with depth. Overall, our results suggest that the thermal, chemical, molecular and isotopic indices of SOM stability were mutually correlated and all showed increasing trend with increasing soil depth in the two alpine ecosystems, although the biological index (as measured by aerobic incubation of root-free sieved soils) showed the opposite results.