Plant resistance based on a gene-for-gene relationship tends not to be durable because virulent strains can emerge through mutation and colonize formerly resistant cultivars over large areas. Our objective was to determine the origin and colonization history of newly virulent strains of the fungus Venturia inaequalis. Four hundred and eighty-one strains from seven multi-cultivar orchards within a 300km wide area were collected from a cultivar carrying the overcome Vf-gene (Vfcv populations) and from non-Vf cultivars (nVfcv populations). Using 9 microsatellite loci, we showed that Vfcv populations were closely related though highly differentiated, indicating they have been recently founded following rare long distance dispersal events from a common origin. Assignment tests revealed that the Vfcv populations had not emerged from any of the nVfcv populations. Vfcv populations had a low diversity and were strongly differentiated from nVfcv populations several years after the first reported breakdown, suggesting reproductive isolation between the two populations.