This study has significantly broadened and deepened the understanding of ecological aspects related to the spread and reproduction of Diplodia pinea as an endophyte, latent pathogen and causal agent of serious disease problems in plantations of Pinus spp. Analyses of genetic diversity in populations using microsatellite data has revealed very high levels of genetic diversity of populations of the pathogen at different spatial levels, ranging from within a single asymptomatic tree to within and between plantations over large geographic areas and in different countries where the fungus has been introduced. Analysis of the structure of the distribution of genotypes and the association of alleles within populations, suggest that sexual recombination is occurring in most environments in the Southern Hemisphere D. pinea populations. This indicates the presence of a cryptic sexual state in this fungus. The genetic diversity was structured and differentiated for regions separated by as little as 65 km to a country and continental scale. The diversity and likely sexual reproduction of D. pinea must complicate control strategies such as selection and breeding for resistance. It is thus essential to strengthen quarantine services aimed at minimizing the risk of introducing additional genotypes of D. pinea. In this regard, understanding the infection and spread between regions is essential. Results of this study demonstrate that this fungus infects seeds, but only at low levels, and is not transmitted vertically via seeds to seedlings. Diplodia pinea was also not isolated from seedlings in three commercial nurseries and open fields in South Africa. These results provide strong evidence that neither seeds nor seedlings are the primary sources of inoculum, but that the pathogen is mainly transmitted horizontally from mature trees and debris left in plantations. Finally extensive sampling conducted as part of this study led to the discovery of the sibling species, D. scrobiculata in South Africa and outside the Northern Hemisphere for the first time.