Monilinia fructicola, M. laxa, and M. fructigena are the fungal pathogens responsible for brown rot disease in stone fruit, which can cause severe preharvest and postharvest losses. The genus Monilinia belongs to the family Sclerotiniaceae, which comprises a large number of plant pathogenic species with a necrotrophic lifestyle. Necrotrophic fungal pathogens kill host cells and subsequently colonize the dead tissue. Induction of programmed cell death can result from the release of metabolites or proteins with phytotoxic activity into the host plants. Such molecules are referred to as effectors. It has been shown that the induction of cell death in several pathosystems is the result of the response of the host to effectors released by nectrotrophs. The identification of effectors can play an important role in breeding for host resistance as it allows one to screen germplasm for susceptible and resistant genotypes, independent of pathogen infection tests. The objective of the present study was to utilize the genome sequence of M. fructicola to identify effector proteins that induce cell death in host plants. The genome was sequenced with PacBio technology and was screened for the presence of genes that encode secreted proteins and more specifically for effector proteins. A set of 134 putative effectors was identified that are presently the subject of functional studies. Several candidate effector genes were cloned into Agrobacterium tumefaciens for transient expression in Nicotiana benthamiana plants. Results indicated that some of the candidates triggered cell death. The identification and increased knowledge about effectors in pathogen virulence can in the future be exploited in effector-based selection of (partially) resistant germplasm. Our research reflects an effort to develop alternative approaches to control brown rot disease and opens a new perspective in breeding for host resistance.