Congenital toxoplasmosis involves Toxoplasma gondii type II strains in 95% of cases in France. We used spatial principal component analysis (sPCA) and 15 microsatellite markers to investigate the spatial genetic structure of type II strains involved in 240 cases of congenital toxoplasmosis in France from 2002 through 2009. Mailing addresses of patients were geo-referenced a posteriori in decimal degrees and categorized into urban or rural areas of residence. No spatial genetic structure was found for type II strains that infected mothers who were living in urban areas, but a global spatial genetic structure was found for those that infected mothers who were living in a rural environment. Our results suggest that sources of infection by T. gondii are different in rural and urban areas in France, and advocate for targeted messages in the prevention of toxoplasmosis according to the type of residence of susceptible people.