The disease known as pitch canker results from infection of Pinus species by the fungus Fusarium circinatum. This fungus also causes a serious root disease of Pinus seedlings and cuttings in forestry nurseries. Pinus radiata and P. patula are especially susceptible to the pathogen, but there are no records of pitch canker on P. patula in established plantations. To date, only planting material of this tree species in nurseries or in plantations at the time of establishment have been infected by F. circinatum. Symptoms of pitch canker have recently emerged in an established P. patula plantation in South Africa and this study sought to determine whether the symptoms were caused by F. circinatum. Isolates from cankers were identified as F. circinatum using morphology and DNA-based diagnostic markers. Microsatellite markers were then used to determine the genetic diversity of a collection of 52 isolates. The entire population included 17 genotypes representing 30 alleles, with a greater number of genotypes collected from younger (three- to six-year-old) than older (12- to 19-year-old) trees. Both mating types of F. circinatum were present, but no evidence of sexual recombination was inferred from population genetic analyses. This is the first record globally of pitch canker on P. patula trees in managed plantations. It is of significant concern to South Africa, where P. patula is the most important Pinus species utilised for plantation forestry.