Apple and stone fruit trees are vital components of Ontario's agricultural landscape. However, since 2016, these trees have been facing alarming mortality rates, exhibiting symptoms collectively referred to as Fruit Tree Decline (FTD) and Rapid Apple Decline (RAD). Despite its widespread occurrence, the exact cause of FTD and RAD remains elusive, with various pathogenic fungi and viruses implicated, along with abiotic stressors such as drought, winter injury and nutrient deficiency. In this study, we sequenced, assembled and annotated the genomes of 12 fungi associated with FTD and RAD syndromes in Ontario, Canada. We present the first and only publicly available assemblies for three ascomycete species including Diplodia intermedia, Diatrype stigma, and Nothophoma quercina. Additionally, we present high-quality reference genome sequences for Diplodia seriata, Didymella pomorum and Neofusicoccum ribis. These genomic resources are valuable for understanding the molecular mechanisms behind FTD and RAD, and for developing strategies for disease prevention and management in fruit trees.