Post‐harvest diseases of apple and pear cause significant losses. Neofabraea spp. and Cadophora spp. infect fruits during the growing season and remain quiescent until disease symptoms occur after several months in storage. Epidemiological knowledge of these diseases is limited. TaqMan PCR assays were developed for quantification of N. alba , N. perennans , C. malorum and C. luteo‐olivacea in environmental samples. Various host tissues, dead weeds and grasses, soil and applied composts were collected in 10 apple and 10 pear orchards in May 2012. Neofabraea alba was detected in 73% of samples from apple orchards and 48% from pear orchards. Neofabraea perennans was present in a few samples. Cadophora luteo‐olivacea was detected in 99% of samples from apple orchards and 93% from pear orchards, whilst C. malorum was not detected in any sample. In apple orchards, highest concentrations of N. alba were found in apple leaf litter, cankers and mummies, and of C. luteo‐olivacea in apple leaf litter, mummies and dead weeds. In pear orchards, N. alba and C. luteo‐olivacea were found in highest concentrations in pear leaf litter and in dead weeds. Substrate colonization varied considerably between orchards. The temporal dynamics of pathogens was followed in four apple orchards and four pear orchards. In apple orchards the colonization by pathogens decreased from April until August and increased from September until December. This pattern was less pronounced in pear. Knowledge on population dynamics is essential for the development of preventative measures to reduce risks of fruit infections during the growing season.