Knowledge of the geographic distribution and frequency of avirulence genes will contribute to the development of strategies to effectively use rice varieties that carry various resistances genes, including combinations of varieties in mixture cropping systems. Here, we analyzed the geographic distribution and frequencies of avirulence genes in rice blast fungus using samples collected from 11 prefectures across Yunnan province, China. A total of 467 single spore isolates were assayed for pathotypes based on their reaction to 20 rice blast resistance monogenic lines. The results revealed that frequencies of avirulence genes among 10 prefectures showed insignificant difference, but frequencies of avirulence genes in Xishuangbanna showed significant differences compared to the remaining 10 prefectures. The avirulence genes Avr-Pi9, Avr-Piz and Avr-Pizt were observed at the highest frequency in blast isolates from the 11 prefectures; their average frequency was greater than 80%. Our results imply that the composition and distribution of rice genetic diversity are more important than climate and other environment conditions for formation and maintenance of rice blast fungus genetic diversity. Using average frequencies, the avirulence genes can be categorized into 4 groups. There were significant differences of frequencies of avirulence genes among different groups, while insignificant differences observed within any group. These results will provide useful information for evaluation of resistance genes and effective management of rice blast disease.