Pinus spp. have a number of fungal endophytes of which the latent pathogen Diplodia pinea is a well-known example. In this study, 12 simple sequence repeat (SSR) markers were used to consider the origin of the southern hemisphere isolates and to evaluate genetic diversity and gene flow between populations of D. pinea. Three populations were isolated from Pinus sp. within the native range of the fungus in the northern hemisphere and three populations were isolated from P. radiata in the southern hemisphere. Populations of D. pinea exhibited low allelic diversity and appear to be clonal, not only regionally, but also across continents. The origin of the southern hemisphere populations could not be determined, as the same alleles are found in all populations. There was no evidence for genetic drift or fixation of alleles in local populations, and some genotypes were found across continents, suggesting both a long asexual history and considerable movement of this pathogen probably assisted by human activities.