Abstract: Objective To characterize the spatio-temporal trends of malaria epidemic in the whole country from 2006 to 2010.Methods Malaria case data were collected spatially at the level of province in the whole country from 2006 to 2010 through the National Disease Supervision Information Management System.Arc GIS 9.0 software was employed to build a malaria database with geographic information and descriptive analyses of spatio-temporal trends of the disease were made based on the strata of five years.Results The malaria incidence rate of the whole country from 2006 to 2010 lowered from 4.60/100 000 to 0.55/100 000,with an average annual incidence of 2.34/100 000.The top three regions reported higher incidence were Anhui, Yunnan,and Hainan province,with the average annual incidence of 27.29/100 000,23.28/100 000,and 11.73/100 000,respectively,and the total incident cases of the three province accounted for 77.48% of all cases in the country during the period.Toally 51 deaths of malaria cases were reported in Yunnan(41) and Sichuan(10) province,accounting for 77.48% of all deaths in the country during the period.Male,farmers,and the elders were the majority of the incident cases and more cases occurred during summer and autumn season.Conclusion The malaria prevalence decreased greatly from 2006 to 2010 in China,and Anhui,Yunnan,Hainan province and Huaihe River Basin zone are the key areas for malaria prevention and control.