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The Altun Mountain National Nature Reserve (AMNNR), characterized by complex topography, is located on the northern edge of the Qinghai-Tibetan Plateau. The stocks of soil organic carbon (SOC) and total nitrogen (TN) are critically important for carbon and nitrogen sequestration in dry alpine ecosystems of the AMNNR, which is a natural laboratory for assessing the carbon and nitrogen storage without human disturbance. We explored the stocks of SOC and TN in soils of different dry alpine ecosystems by sampling 23 sites across the AMNNR during 2013. The results showed that the SOC and TN stocks of AMNNR varied significantly with ecosystem types. The SOC stocks of 0-15cm were highest in the alpine wet meadow (7.96kg/m(2)), followed by alpine steppe (2.63kg/m(2)). The stocks of SOC and TN in 0-5 and 5-10cm soils of alpine wet meadow were significantly (P<0.05) higher than those in the soils of other dry alpine ecosystems. In the whole AMNNR, total storage of SOC and TN were approximately 80.97 and 4.48Tg, 34.25% of SOC and 24.01% of TN were stored in the alpine steppe, 21.51% of SOC and 26.01% of TN were stored in the alpine scrub, the largest ecosystem in the AMNNR. Our findings suggested it is important to protect the soil and vegetation of the dry alpine ecosystems, particularly the alpine wet meadow and alpine scrub to promote the carbon storage.