The genetic diversity of Toxoplasma gondii varies in different geographical regions. Isolates of T. gondii in South America, for example, are genetically and biologically divergent from those in North America and Europe, where the population structure is highly clonal and composed mainly of 3 distinct lineages, i.e., Types I, II, and III. However, little is known of the T. gondii genotypes in the People's Republic of China. Toxoplasma gondii infection in pigs causes significant economic loss and presents a risk for human infection. We conducted a survey to determine the genetic diversity of this parasite in slaughtered pigs from Yunnan Province, southwestern China. In total, 412 DNA samples were extracted from hilar lymph nodes and livers of pigs from slaughterhouses in Yunnan Province in southwest China, 56 of which were found to be positive for the T. gondii SAG3 gene. These positive DNA samples were typed at 10 genetic markers, including 9 nuclear loci, i.e., SAG1, SAG2, SAG3, BTUB, GRA6, L358, PK1, c22-8, c29-2, and an apicoplast locus Apico. Of these, 5 isolates were genotyped with complete data for all loci. Only 1 genotype (ToxoDB 9) was identified, previously reported as a widespread lineage from pigs, cats, and human patients in China. The results indicate that this genotype may be the major T. gondii lineage in China and possibly all of eastern Asia. This is the first report of genetic typing of T. gondii isolates from pigs in China's southwestern Yunnan Province, the results of which have implications for the prevention and control of T. gondii infections in humans and other animals.