In wetland ecosystems, methane is actively utilized by methanotrophs. The immobilized methane carbon is then passed on to other organisms such as grazers. Here, we traced the incorporation of methanotrophic biomass into eukaryotes in a rice field soil using phospholipid fatty acid stable-isotope probing (PLFA-SIP). Addition of 13C-labeled cells of five methanotrophs to soil (5 × 107 cells g−1 soil) did not affect the CO2 release rate, but significantly increased the carbon isotopic ratio within 24 h. In 48 h, 2–7% of the added bacterial biomass carbon was detected as 13CO2. The soil with Methylobacter luteus released the highest amount of 13CO2, comparable to that with Escherichia coli. The amount of polyunsaturated PLFAs (C18:3ω6c and C20:4ω6c) was not affected by the addition of bacterial cells to soil, but their carbon isotopic ratio increased significantly within 24–48 h. The extent of 13C-enrichment in PLFAs differed between the added methanotrophs, with the highest labeling upon addition of M. luteus. The relative abundance of 13C-labeled C18:3ω6c to C20:4ω6C also differed between the strains. The results indicated that the eukaryotes in soil, probably protozoa, preferentially graze on specific methanotrophs and immediately incorporate their biomass.