The population structure of Toxoplasma gondii is characterized by contrasting geographic patterns of strain diversity at different spatial scales: global, regional and even local scales in some regions. The determinants of this diversity pattern and its possible evolutionary mechanisms are still largely unexplored. This review will focus on three main dichotomies observed in the population structure of the parasite: (1) domestic versus wild, (2) South America versus the rest of the world and (3) intercontinental clonal lineages versus regional or local clonal lineages. Here, the impact in terms of public health of this remarkably contrasting geographic diversity of T. gondii populations is discussed, with emphasis on the role of globalization of exchanges that could lead to rapid evolution of T. gondii population spatial structure and new challenges in a One Health context.