Elevated atmospheric CO2 was often shown to stimulate belowground C allocation, but it is uncertain if this increase also alters the structure of soil microbial communities. Here, we assessed the effects of nine years of CO2 enrichment on soil microbial communities of an alpine treeline ecosystem with 35-year-old Lath decidua and Pinus mugo ssp. uncinata trees. We also tracked the C-13 signal of supplemental CO2 in soil-respired CO2, microbial biomass, and phospholipid fatty acids (PLFA) in undisturbed mor-type organic layers. We found a persistently increased soil CO2 efflux (+24% on average), but negligible effects of elevated CO2 on the biomass and community structure of soil microorganisms under both tree species determined with PLFA and T-RFLP (terminal restriction fragment length polymorphism). The C-13 tracing over 9 years revealed that 24-40% of the soil microbial biomass was composed of 'new' plant-derived C. PLFA from gram-negative biomarkers did not significant shift in C-13 by the CO2 addition, while those of gram-negative bacteria were significantly altered. The highest C-13 signals in individual PLFA was found in the fatty acid 18:26)6,9 with 65-80% new C, indicating that new plant-derived C was primarily incorporated by soil fungi. However, CO2 enrichment did not affect the production of mycelia biomass and the structure and composition of the fungal communities analysed by high-throughput 454-sequencing of genetic markers. Collectively, our results suggest that C flux through the plant soil system will be accelerated but that the biomass and composition of microbial communities will be little affected by rising atmospheric CO2 in organic matter rich treeline soils.