Diverse sources of infection and cryptic recombination revealed in South African Diplodia pinea populations

► Population diversity and structure of Diplodia pinea in South Africa at different spatial scales from single trees to plantations were characterized. ► Thirteen microsatellite markers have been used confirming that they are powerful tools to study population genetics of D. pinea. ► Diplodia pinea has a high level of gene and genotypic diversity in South Africa. ► Recombination is occurring in D. pinea and it most likely has a cryptic sexual state. ► Wound-associated pine tree die-back appears to be caused by clones of the pathogen occurring in narrow time frames as compared to endophytes. ► Genetic diversity of D. pinea in asymptomatic pine tree is higher than from diseased trees.