Since its introduction into Europe in the first half of the 20th century, Cryphonectria parasitica has been gradually spreading across the natural range of the sweet chestnut (Castanea sativa Mill.), infecting the trees and causing lethal bark cankers. Serendipitously, a hyperparasitic Cryphonectria hypovirus 1 (CHV1), which attenuates C. parasitica virulence in combination with more tolerant European chestnut species, was able to ward off the worst effect of the disease. In North America, unfortunately, the native Castanea dentata is now functionally extinct since it occurs only as root sprouts in eastern deciduous forests where it was once dominant. In our work, we investigated changes in C. parasitica populations over time and the regional variability in chestnut populations’ tolerance toward the blight disease. While vegetative compatibility (vc) type diversity and prevalence of hypovirulence remained similar as in previous studies, in the Buje population, unlike in previous studies, we were unable to find any hypovirulent fungal strains. The most common vegetative compatibility types (vc types) were EU-1, EU-2 and EU-12. However, several rare EU-types were found, including one previously unreported: EU-46. By inoculating several C. parasitica strains on tree stems from several chestnut populations, we observed that the induced lesion size was affected by the type of inoculum (CHV1-free or CHV1-infected), genotype-related individual chestnut stem and chestnut stem population of origin-related variability. The largest lesions were induced by CHV1-free fungal isolate DOB-G: 20.13 cm2 (95% C.I. 18.10–22.15) and the smallest by CHV1-infected L14/EP713: 2.49 cm2 (95% C.I. 1.59–3.39). Surprisingly, the size of the lesions induced by other CHV1-infected strains fell somewhere in between these extremes. The size of induced lesions was dependent on the population of origin as well and ranged from 11.60 cm2 (95% C.I. 9.87–13.33) for stems from the Moslavačka gora population to 17.75 cm2 (95% C.I. 15.63–19.87) for stems from Ozalj.