Methane emission can be affected by soil fertility, but little is known about the influence of soil phosphorus (P) nutrition on methane production and oxidation processes. In this study, a pot experiment was conducted to explore the effects of P amendments on activity, abundance and community composition of soil methanogens and methanotrophs using P deficient paddy soil. The abundance and community composition of methanogens and methanotrophs, methane production and oxidation potentials were investigated by real-time quantitative PCR, Miseq high-throughput sequencing and biochemical assays, respectively. The results showed that although P amendments induced increases of both methanogenic and methanotrophic abundances and potential activities within bulk soils, the increases were relatively small. In contrast, P applications resulted in large and significant increases in the copy numbers and potential activity of methanogens within rhizosphere soils, whereas, this phenomenon was not detected for methanotrophs. Moreover, the methanogenic community structure remained similar amongst the P amendment treatments for both rhizosphere and bulk soils. For methanotrophs, P application induced clear shifts in the community composition within rhizosphere soils but not in bulk soils, where the relative abundance of type I methanotrophs increased whilst type II decreased. Our data indicate that the application of phosphate to P deficient paddy soils could preferentially stimulate the abundance and activity of methanogens over methanotrophs within the rice rhizosphere. Ultimately, improving plant growth by P input may accelerate methane emissions through stimulating rhizosphere methanogenic populations without a concomitant increase in the methanotrophic compartment.