The southern and tropical southeastern regions of the Yunnan Province in southwestern China have similar monsoonal climates and lowland tropical rain forest vegetations. The floras of both regions are dominated by tropical floristic elements (78.3% in southern Yunnan and 68.83% in southeastern Yunnan), and both belong to the Indo-Malaysian flora at the northern margin of tropical Asia. However, some temperate East Asian characteristic families are well represented in the flora of tropical southeastern Yunnan, while families characteristic of tropical Asia are well represented in the flora of southern Yunnan. Additionally, there are 14 mainly east Asian families in tropical southeastern Yunnan that are not found in southern Yunnan. Although the two regions share 80% of their genera, 237 genera are restricted to southern Yunnan, and 349 genera to tropical southeastern Yunnan. Furthermore, 57 genera with an East Asian distribution, 53 genera with a North temperate distribution, 22 genera endemic to China, and 17 genera with an East Asia and North America disjunct distribution are found only in tropical southeastern Yunnan. The flora of tropical southeastern Yunnan is more closely related to Eastern Asian flora, while the flora of southern Yunnan is more closely related to Indo-Malaysian flora. The divergence of the flora is well supported by the geological history of the region; the flora of tropical southeastern Yunnan was mainly derived from the South China Geoblock, while the southern Yunnan flora derived from the Shan-Thai Geoblock.