Rodents play an important role in the transmission of Toxoplasma gondii; however, little is known about the seroprevalence and genetic diversity of T. gondii infection in rodents in Yunnan Province, China. In this study, we examined the seroprevalence and genetically characterized T. gondii infection in naturally infected rodents in Yunnan Province between March and July 2016. In total, 261 serum samples were collected from rodents in the Jingha district, Xishuangbanna Dai Autonomous Prefecture, Yunnan Province, and examined for T. gondii antibodies by modified agglutination test (MAT) at a 1:20 cut-off, with titers of 1:20 in 24 samples, 1:40 in 10, 1:80 in 10, and 1:160 in 4. Thirty-two of 261 (12.26%) serum samples were positive for T. gondii by MAT. In total, 751 rodent brain samples were examined by semi-nested PCR; 46 (6.13%) were positive for the T. gondii B1 gene, 2 of which showed complete genotyping results for all 11 polymorphic loci (SAG1, SAG2, alt.SAG2, SAG3, BTUB, GRA6, L358, PK1, C22-8, C29-2, and Apico). The 2 samples were characterized to represent ToxoDB#137 ( http://toxodb.org/toxo/). These findings enriched the epidemiological and genetic diversity of T. gondii in China and have implications for the better prevention and control of T. gondii infection in humans and animals.