Methane-oxidizing bacteria (methanotrophs) consume a significant but variable fraction of greenhouse-active methane gas produced in wetlands and rice paddies before it can be emitted to the atmosphere. Temporal and spatial dynamics of methanotroph populations in California rice paddies were quantified using phospholipid biomarker analyses in order to evaluate the relative importance of type I and type II methanotrophs with depth and in relation to rice roots. Methanotroph population fluctuations occurred primarily within the top 0–2 cm of soil, where methanotroph cells increased by a factor of 3–5 over the flooded rice-growing season. The results indicate that rice roots and rhizospheres were less important than the soil–water interface in supporting methanotroph growth. Both type I and type II methanotrophs were abundant throughout the year. However, only type II populations were strongly correlated with soil porewater methane concentrations and rice growth.