Fruit flies (Diptera: Tephritidae) and their geographic distribution were investigated by systematic trapping and large-scale surveys of damaged fruit in 2003-2007 in more than 100 counties in Yunnan, China. Twenty five species of Tephritidae were identified as the major fruit fly pests in Yunnan. Cluster analysis was used to explore relationships between the geographical distribution of the Yunnan Tephritidae species and several characteristics of the region′s physical geography. Overall, five zoogeographical zones were identified: Xishuangbanna and Dehong basin valley, south margin of Yunnan middle-low mountain and strath, southwestern Yunnan mountain plateau and valley, east-central Yunnan plateau and karst plateau, and northern Yunnan plateau mountain zone. Temperature was the critical condition in explaining the geographic distribution of the fruit flies in Yunnan. Tephritidae species diversity increased along a gradient from north to south in Yunnan, with the highest number of Tephritidae species recorded in the valley zones in the southwestern Yunnan. This is the first study to demonstrate the relationship of fruit fly pest diversity to geographical features in Yunnan.