Studies on the gene of the target protein of QoI fungicides (cytochrome b) in Monilinia laxa, M. fructigena and M. fructicola showed that the occurrence of the most important resistance mechanism to QoI fungicides, the G143A mutation, is relatively unlikely in M. laxa and M. fructicola. This is due to the presence of an intron sequence directly after codon 143. A mutation in codon 143 would presumably lead to incorrect mRNA maturation and consequently to a non-functional protein. No introns were found directly before or after codon 143 in M. fructigena, therefore the G143A mutation may be possible. Intron sequences have not been detected in immediate vicinity to the codons 129 and 137 in all three species, so the occurrence of the mutations F129L and G137R could be possible. Based on the differences in the intron-exon organization of the cytochrome b gene, a rapid, sensitive and reliable PCR assay for identification and differentiation of the 3 Monilinia species was developed.