We review herein studies concerning the genomic polymorphism of Toxoplasma gondii including 3 clones (1 linked with mouse pathogenicity), 5 zymodemes, and 13 schizodemes. Because mutations occur with some frequency and several allelic configurations are present in isolates grown in the same environment, we conclude that many of the mutations may not be affected by selection pressure. However, the gametocyte-forming ability is under selection pressure from the hose and depends on the development of bradyzoites in tissue cysts. After prolonged multiplication exclusively in the tachyzoite stage in mice and, possibly, in patients the gametocyte-forming ability may be lost. To avoid this genomic change, isolates should be passed in the laboratory, permitting bradyzoite and tissue-cyst formation. Mouse pathogenicity is selected for during mouse passage. We find no major genomic instability justifying species or subspecies distinctions.