Reduction patterns of Plasmodium falciparum and P. vivax malaria transmission and the role of an integrated strategy of case management and vector control are compared between different ecological zones. The epidemiology of malaria in Hainan and Yunnan provinces was disparate, even though distinct malaria control strategies have been adapted to different situations based on risk group, vector behaviours, local health infrastructure, and environmental conditions. The island Hainan appears to be victorious in eliminating malaria. However, there is still a long way to go to prevent the reintroduction of malaria in Hainan province and eliminating malaria in the border areas of Yunnan province. This review of the experiences and challenges from malaria control to elimination in Hainan and Yunnan provinces of southern China will provide a basis for the future elimination of malaria in the whole country.