Toxoplasma gondii is an intracellular protozoan parasite which imperils the health of almost all warm-blooded animals, including humans. The objective of this study was to determine genetic characterization of T. gondii in free-living Microtus fortis (reed vole) in Jilin province, northeastern China. A total of 104 DNA samples, 74 from Gongzhuling and 30 from Baicheng, were extracted from lung tissues of M. fortis, and 56 (53.8%) of them were positive for T. gondii by semi-nested polymerase chain reaction of the B1 gene. These positive DNA samples were typed at 10 genetic markers including SAG1, 5′- and 3′-SAG2, alternative SAG2, BUTB, GRA6, L358, PK1, c22-8, c29-2, and Apico. Four samples were successfully genotyped at all genetic loci and grouped to 2 distinct genotypes; 2 samples belonged to ToxoDB Genotype no. 10 (Type I) and the other 2 presented ToxoDB Genotype no. 9 (http://toxodb.org/toxo/); 4 samples were genotyped at 8 genetic loci, in which 2 samples belonged to ToxoDB Genotype no. 10 and 2 presented ToxoDB Genotype no. 9. To our knowledge, this is the first report of genetic typing of T. gondii from free-living M. fortis in northeast China. The results suggest that the Type I and ToxoDB Genotype no. 9 could be a potential risk factor for transmission through the reed vole in this region.