Toxoplasma gondii is an intracellular Apicomplexan parasite that infects a wide range of warm blooded animals, including human, and has complex life cycle and pathogenic mechanisms. Although T. gondii is the only species recognized in the Toxoplasma genus, research on population genetic structure has shown its geographic genetic diversity. So far 232 genotypes have been identified by multilocus polymerase chain reaction-restriction fragment length polymorphism or microsatellite genotyping from both animals and human. T. gondii strains in North America typically possess types 2, 3 and 12 (found mainly in wild animals) clonal lineages, while types 2, 3, and 1 are common in Europe, and types 2 and 3 are common in Africa. These findings suggest a strongly clonal population structure in these regions. However, strains in South America are genetically more diverse, predominated by types Br I , Br II, Br III, and Br IV. Recent research has shown that the Chinese 1 (ToxoDB#9) genotype is dominantly circulating in the mainland of China, and shares the polymorphic ROP16I/III with types 1 and 3, and GRA15II with type 2. In this review, we summarized geographically the genotypes, host immune responses, and the pathogenic mechanisms of T. gondii strains, to provide basis for further research on genotype/effector-related pathogenic mechanism as well as biological and epidemiological studies of T. gondii.