Phytoplasmas causing diseases of woody plants in native environments and agricultural systems are responsible for considerably economic and environmental damage. In Central and Southern Europe, phytoplasma diseases of apple (Malus domestica: Apple proliferation, AP) and grapevine (Vitis vinifera: Bois noir, BN and Flavescence dorèe, FD) are widespread and impact quantity and quality of the fruits. The ecology of phytoplasma diseases is complex and involves one or more insect vectors and in some cases alternative host plants. Phytoplasma densities in infected plants and expression of symptoms can vary considerably among seasons, and remission of symptoms occurs frequently. Disease control by pesticide application generally is not very efficient, therefore a polyphasic control strategy using a mix of agronomical, chemical and biological strategies needs to be developed for each disease. In the case of Bois noir e.g., the population density of the vector Hyalesthes obsoletus is related to the presence of its main host plants Urtica dioica and Convulvulus arvensis in the understory of the vineyards, which can be managed by agronomical methods. Application of foliar fertilizer showed no significant effect on BN-infected grapevines. AP-infected apple trees were treated with four bio-active compounds (Acibenzolar-S-Methyl, Harpin protein, Prohexadione-Ca and Cyanamide) over a three-year period, but their effects on symptom expression were only limited and transient.