Apples are susceptible to infection by the fungal pathogen, Phlyctema vagabunda syn. Neofabraea alba. Infections are symptomless on fruit in the orchard, but pruning wounds result in disintegration of the outer tissues progressing from the wound and leading to ‘fiddle string’ symptoms of exposed bast fibres. Postharvest, P. vagabunda causes bull’s eye rot which expresses during long-term storage and renders fruit unsaleable. Of interest is whether peaks of spore production are associated with the occurrence of infections, or whether plant factors are the major factor influencing infection timing. To collect spores, rain traps and vertical splashometers were placed in apple orchards and retrieved at monthly intervals for two seasons. DNA was extracted from resultant rainwater, and from cellophane from the splashometers. TaqMan qPCR and primers specific to P. vagabunda were used to quantify the pathogen DNA, then converted to spore counts. Peaks of spore production occurred late in the season, coinciding with fruit infections. In winter, when apples are pruned, spores were available for infection but at lower levels. Our results showed that spores were always available; peaks of spore production could be explained by a hypothesised disease cycle, and that fruit and wound susceptibility were the predominant drivers of infection timing.