The sweet cherry industry has grown substantially in recent years and high quality fruit is required for domestic and export markets. Incidence of rot can be high in some seasons and optimal management is not well understood. Several pathogens are known to cause rot in sweet cherry fruit, primarily including Monilinia fructicola, Monilinia laxa and Botrytis cinerea. The Monilinia spp. cause brown rot while B. cinerea causes grey mould, however the symptoms caused by these three pathogens can be difficult to distinguish and all result in substantial losses to fruit quality. Key times of risk are not currently well understood in Australian orchards but factors such as inoculum presence and weather-based infection likelihood can be determined. Relative abundance of rot pathogens in Australian sweet cherry orchards has not been well documented to date. During a three year project it was clearly established that Botrytis cinerea was the dominant rot pathogen in the orchards surveyed in southern Tasmania, while Alternaria alternata was a dominant cause of rot in orchards of Orange and Young in NSW. Temperature and wetness durations conducive to fruit infection (and the impact of fruit susceptibility) were modelled for B. cinerea, M. laxa and M. fructicola. Latent infection was quantified for flowers and developing fruit but there was no significant relationship with rot at harvest. A molecular method was developed to quantify spores of B. cinerea, M. laxa and M. fructicola from spore trap samples and peaks of high relative abundance occurred throughout the season from flowering to harvest.