Toxoplasma gondii infections are prevalent in humans and animals worldwide. In North America and Europe, T. gondii is highly clonal, consisting of three distinct lineages (Types I, II and III), whereas in South America, T. gondii is highly diverse with a few lineages expanded in the population. However, there is limited data on the diversity of T. gondii in Asia. Here we report the genetic characterization of T. gondii isolates from different hosts and geographical locations in China using the multilocus PCR-RFLP. A total of 17 T. gondii isolates from humans (3 strains), sheep (1 strain), pigs (5 strains) and cats (8 strains) were typed at 10 genetic markers including 9 nuclear loci SAG1, SAG2, SAG3, BTUB, GRA6, L358, PK1, c22-8, c29-2 and an apicoplast locus Apico. Four genotypes were revealed, including three previously reported and one new genotype. Three isolates belong to the clonal Type I lineage, one isolate belongs to the clonal Type II lineage, and the rest 13 isolates are grouped into two genotypes. This is the first report of genetic typing of T. gondii isolates from different hosts and geographical locations in China using a number of genetic markers, which has implications for the studies of population genetic structures of T. gondii, as well as for the prevention and control of T. gondii infections in humans and animals in China.