A comprehensive study of the population biology of Cryphonectria parasitica, the causal agent of chestnut blight, is required to understand the spread of the epidemic in Europe and its natural regulation by the Cryphonectria hypovirus-1 (CHV-1). With this objective in mind, the diversity in vegetative compatibility (vc) types and mating types of C. parasitica populations was assessed in 43 chestnut sites in western France and northern Spain. Isolates were sampled in three regions along the Pyrénées mountains (Hautes Pyrénées, Pyrénées Atlantiques and Navarra) and in two regions north of the Pyrénées (Landes and Dordogne). There were 61 vc types observed in 682 isolates sampled. Ninety-five isolates (14%) could not be assigned to any one of the previously known European vc types. The finding of 47 incompatible vc types confirmed that the genetics of vegetative compatibility could not be totally accounted for by six diallelic vic genes. The two idiomorphs of the mating type gene were detected in all regions, indicating that sexual reproduction could occur within and between vc types. In all regions except Dordogne, C. parasitica populations were dominated either by the vc type EU-66 or EU-72. Neither vc type has been reported elsewhere in Europe, which suggests that two different introductions of C. parasitica have occurred in the study area. In Dordogne, populations were dominated by EU-33 and EU-2, and to a lesser extent EU-66 and EU-72. The low diversity in vc types for most of the C. parasitica populations provides good opportunities for natural regulation in forest coppices and for biocontrol with CHV-1 in orchards.