According to the latest archaeological discoveries in the low Yangtze River Delta of China, in history rice cultivation can trace back to B. C. 4 000 in China. A mini-pot-culture experiment was carried out to evaluate effects of rice cultivation on microbial functional diversity and ammonia-oxidizing bacterial number in ancient paddy soils that have been buried under-ground for thousands of years, and in present paddy soil as well. A huge population of ammonia-oxidizing bacteria (AOB), about 0.416～1.235 MPN mg^-1 dry soil, was observed in the present paddy soil, while only a limited number of AOB, about 0.013～0.055 MPN mg^-1 dry soil, was detected in the ancient paddy soils after incubation for one or two months in greenhouse. Rice cultivation without N fertilization decreased the number of soil AOB significantly, while rice cultivation with ammonium sulfate fertilization increased its number within a short period of time, but sodium nitrate fertilization did not show any significant effect on soil AOB. The present paddy soil was much lower than the ancient paddy soils in carbon-source utilization capability, and in Shannon index, Simpson index and McIntosh index of microbial community to a varying extent. Rice cultivation, however,significantly increased carbon-source utilization capability of the microbial community as a whole in the present paddy soil, and raised the three indices therein up to the level of the ancient soils. The increase was slowed down by N fertilization. Rice cultivation and N fertilization did not significantly affect these functional diversity indices of the microbial community in the ancient paddy soils, and no significant difference was observed between the 3 320 a and 6 280 a ancient paddy soils.