The clonal structure of Magnaporthe oryzae populations was observed in various countries. This information was used to propose new resistance deployment strategies. However, our understanding of how new virulent races appear and spread remains limited. Population genetic analyses, with neutral and selected markers, provide tools to evaluate such events. We used microsatellite markers to study populations at the worldwide scale. We observed three major genetic groups. Two groups include isolates of only one mating each. The third group includes isolates of both mating types. During natural epidemics spores disperse over short distances (1-5 m). This is likely to cause the partial geographic structuring we observed. However, long distance migrations are possible through the transportation of infected seeds. We observed that, in some cases, one population is more closely related to populations from other continents than from a population from the same area. Long distance migration was also confirmed by studying the distribution of the genotypes of the cloned avirulence gene ACE1. Two major virulent genotypes were identified. These genotypes appeared by a complex duplication/deletion event. These two genotypes are widely distributed over different continents. Altogether, these results suggest a unique apparition event followed by long distance migrations of virulent genotypes.