Cyclaneusma needle-cast (CNC) is a disease of Pinus radiata caused by the ascomycetous fungus Cyclaneusma minus. This disease effects plantations in both New Zealand and Australia, although the deployment of less susceptible genotypes of pine has reduced its impact over time. It has been long known that morphological variation exists within the population and two morphotypes have been characterised; C. minus “simile” and C. minus “verum”. A recent molecular analysis has shown that these two morphotypes are most likely different species. It is not known if one or both of these morphotypes are responsible for disease in P. radiata plantations in New Zealand. New tools for molecular differentiation of these morhotypes showed that C. minus simile is more commonly isolated or detected in infected trees than C. minus verum, and is more common in areas where disease is most prevalent. Most of the C. minus simile isolates, collected from 1969 to 2008, were isolated from the North Island, whereas most C. minus verum isolates were isolated from the South Island of New Zealand. However, a third type of strain has also been isolated which is genetically divergent from both the verum and simile morphotypes. While this collection of isolates is very small, it is interesting to note that the majority of these isolates came from needles that appeared healthy and green and were collected at the same as needle displaying symptoms of CNC from adjacent trees in the same forest. Understanding the genetic diversity and population structure of this group of fungi will ultimately lead to better outcomes for control of CNC.