The 18O-labelled-water incubation approach is the latest widely used method for soil microbial carbon use efficiency (CUE) estimation. This approach assumes oxygen used for microbial DNA synthesis is from growth medium water. However, whether the oxygen might be from oxygen gas (O2) is unknown. Here we compared the results of 18O-labelled water and 18O-labelled O2 incubation experiments following the standard procedure of soil microbial CUE measurement. Results indicated that 99.25% of the oxygen atoms in the newly synthesized microbial DNA after 48 h of incubation were derived from applied water, while 0.75% of the oxygen atoms were derived from O2. Our study suggests the contribution of O2 to microbial DNA synthesis is negligible during short-term incubation and the 18O-labelled-water approach is reliable for estimating soil microbial CUE for the tested forest soil.