Totally 14,491 malaria cases and 59 741 suspected cases with 12 deaths were reported by the annual case reporting system in 1171 counties of 23 Provinces/Municipalities/Autonomous Regions (P/M/A) in 2009, and the annual incidence was 0.11/10,000. Through the internet reporting system, 14,140 malaria cases were reported from 956 counties of 30 P/M/ A. The number of malaria cases and the rank of P/M/A were basically in concordance in the two systems. Among the 1171 counties with reported malaria cases, 4 counties with an incidence of more than 10/10,000 distributed in Yunnan (3 counties) and Tibet (1). There were 59 counties in which the malaria incidence was between 1/ 10,000 and 10/10,000. A total of 1027 Plasmodium falciparum malaria cases accounted for 7.1% of the total cases, of which 87.3% (897) were imported cases reported in 326 counties/cities of 21 P/M/A. Indigenous falciparum malaria was found in 18 counties/cities of Yunnan and Hainan Provinces, of which 16 counties/cities were in Yunnan and 2 counties/cities were in Hainan, 3 or 6 less respectively in comparison to that of 2008. No focal outbreaks occurred in the whole country in 2009. Although a considerable decrease in malaria incidence contributed to the implementation of the National Malaria Control Program and the project supported by the Global Fund to Fight AIDS, Tuberculosis and Malaria, Yunnan and Hainan Provinces are still the relatively high transmission areas. Yunnan ranked No.2 in the country in terms of the number of cases, while Hainan ranked down to No.6 by malaria incidence in 2009. Three thousand nine hundred and twenty two malaria cases were reported from the two provinces in 2009, accounting for 27.1% of the total reported cases in the country. There were 3 237 cases with 3 deaths reported from Yunnan, the incidence was 0.96/10,000, a decrease of 17.2% than that in the last year. Among the reported cases, 567 were falciparum malaria with 49.7% imported cases. The number of reported cases in Hainan was 685, with an incidence of 0.79/10,000, 63.8% decrease than the last year. In central China, the resurgence of malaria was suppressed and the number of malaria cases was considerably decreased in 2009, but the incidence in Anhui Province has still been the first in the country. A total of 5 918 malaria cases were reported from Anhui Province in 2009, accounting for 40.8% of the total cases in the country, with an incidence of 1.19/10,000 which decreased by 50.8% than that in 2008. The number of reported cases in Henan Province was 1 611, decreased by 40.8% in incidence. Hubei Province reported 709 malaria cases with an incidence of 0.12/10,000, decreased by 34.8%. There were 389 cases reported from Jiangsu Province, decreased by 41.8% compared to that in 2008. Cases reported from other P/M/A occupied about 13.4% of the total. Above hundred were reported from Shandong and less than 100 cases were reported from each of Fujian, Chongqing, Shanghai, Jiangxi, Liaoning, Shaanxi, Jilin, Heilongjiang, Gansu and Tibet in 2009. In summary, the re-emergence of malaria has been restrained through several years' efforts, but malaria is still an important problem of public health in China, especially in the southern and central parts. Yunnan and Hainan still face the spread of Plasmodium falciparum, especially imported malaria in the border areas. In the central parts of the country, Anhui Province is still with the highest incidence in 2009. In addition, imported malaria cases in those provinces with a low transmission or without local transmission may become a new challenge to the National Malaria Control Program.