Aerobic anoxygenic phototrophic bacteria (AAnPB) are recognized as an important group driving the global carbon cycling. However, the diversity of AAnPB in terrestrial environment remains largely unknown as well as their responses to the elevated atmospheric CO2. By using culture-independent techniques, the diversity of AAnPB in paddy soil and the changes in response to the rising atmospheric CO2 were investigated within China FACE (Free-air CO2 enrichment) platform. There was a phylogenetically diverse AAnPB community with large population size residing in paddy soil. The community structure of AAnPB in bulk and rhizospheric soils stayed almost identical, while the population size was higher in rhizospheric [2.0–2.5 × 108 copy number of pufM genes g−1 dry weight soil (d.w.s.)] than that in bulk (0.7–0.8 × 108 g−1 d.w.s.) soils. Elevated atmospheric CO2 appeared to significantly stimulate AAnPB abundance (up to 1.4–1.5 × 108 g−1 d.w.s.) and result in a higher AAnPB percentage in total bacterial community (from 0.5% up to 1.5%) in bulk soil, whereas no significant effect was observed in rhizospheric soil. Our results would extend the functional ecotypes of AAnPB and indicate that environmental changes associated with the rising atmospheric CO2 might affect AAnPB community in paddy soil.