Toxoplasma gondii is a zoonotic protozoan with a global occurrence. Exploring the population structure of T. gondii is important to understand its worldwide distribution and the determinants of its evolution. To date, in Europe and North America, most of isolated strains appeared to belong to two main weakly pathogenic clonal lineages: Types II and III. Conversely, studies from South America showed evidence for a substantial genetic diversity in this continent. Other genotypes were described in Asia and Africa. Determinants of this spatial structure are still poorly understood. Moreover, globalization of exchanges could drive rapid evolution of T. gondii population spatial structure, with unknown health outcomes. Our aim was to investigate the possible role of maritime trade in shaping current T. gondii populations structure. In this study, 2040 animals from Senegal were screened for T. gondii infection in two ports cities founded by French colons (Dakar and Saint-Louis) and one inland region (Kedougou). Overall, 77 isolates were obtained by mouse bioassay and strain virulence was characterized. Genotyping using 15 microsatellite markers revealed the presence of a highly contrasting diversity between port cities and the inland Kedougou. In Saint-Louis and Dakar, we found a large predominance of lineages which are non-virulent for mice, whereas the mouse-virulent Africa 1 lineage was predominant in inland Kedougou. In port cities of Senegal, the invasive house mouse has been introduced by European sailors since colonial time and has become the predominant putative reservoir of T. gondii in these port cities. At the opposite, the native African Mastomys natalensis is the predominant putative reservoir of T. gondii in Kedougou. The possible occurrence of distinct host specialization to the different T. gondii lineages may explain the contrasted geographical structure in T. gondii populations between coastal and inland regions, which appear to spatially correlate with host resistance.