Biscogniauxia mediterranea is a pathogenic fungus associated with Quercus species causing charcoal canker disease in forests. Its phenotypic and genetic variability has been well studied in Tunisia but little is known about its demographic history. Population dynamic of B. mediterranea was evaluated among 30 isolates from different cork oak forests in Northwestern Tunisia. The genetic structure analyzed with two DNA markers (ITS and tef-1α) showed low genetic differentiation associated with high genetic flow among populations. The polymorphism analysis showed low nucleotide diversity but high haplotypic diversity among and within B. mediterranea populations which could be due to rapid growth from a small ancestral population. This hints at recent population growth after a period of decline likely due to a catastrophic event involving fires and human-induced tree cutting. The resulting genetic diversity within populations primarily arises from the emergence of new haplotypes. Overall, this study provides insights into the polymorphism of B. mediterranea and its potential adaptive strategy.