Introduction Anaerobic ammonium oxidation (anammox) plays a vital role in the global nitrogen cycle by oxidizing ammonium to nitrogen under anaerobic environments. However, the existence, abundance, and diversity of anammox bacteria between different temperatures are less studied, particularly in purple paddy soils. Methods 13 C-DNA stable-isotope probe combined with Illumina MiSeq high-throughput sequencing was employed to explore soil abundance and diversity of anammox bacteria. In doing so, 40–60 cm depth soils from typical purple paddy soils in Chongqing, southwest China, were cultured under 12 CO 2 -labeled and 13 CO 2 -labeled at 35°C, 25°C, 15°C, and 5°C for 56 days. Results and Discussion Anammox bacteria were not labeled at all by 13 CO 2 at 5°C. The highest abundance of anammox bacteria was found at 25°C (3.52 × 10 6 ~3.66 × 10 6 copies·g −1 dry soil), followed by 35°C and 15°C (2.01 × 10 6 ~2.37 × 10 6 copies·g −1 dry soil) and almost no increase at 5°C. The relative abundance of Candidatus Jettenia sp. was higher at 25°C and 15°C, while Candidatus Brocadia sp. was higher at 35°C and 5°C. Our results revealed differences in anammox bacteria at different temperatures in purple paddy soils, which could provide a better understanding of soil N cycling regulated by anammox bacteria.