Polymerase chain reaction integrated with sequence analysis was carried out to investigate the natural Anaplasma phagocytophilum infection in ticks and rodents from a forest area of Jilin Province, China. Four (4.0%) of 100 Ixodes persulcatus and 2 (0.7%) of 286 Dermacentor silvarum ticks collected by flagging vegetation were positive. Nine (8.8%) of 102 rodents were infected, as well as 2 (2.8%) of 71 I. persulcatus parasitizing on 25 rodents. The nucleotide sequences of 1442-bp A. phagocytophilum 16S rRNA gene amplified from rodents and ticks were identical to each other and to that previously reported in Heilongjiang Province of China (GenBank accession no. AF205140), but different from those of other countries. The sequences of 357-bp partial citrate synthase gene from the above specimens were homologic, and varied from known A. phagocytophilum agents. These findings add new information on the ecologic features of A. phagocytophilum and indicate the threat of anaplasmosis in the area.