The population structure of Xanthomonas arboricola pv. pruni (Xap), the causal agent of the bacterial canker/leaf and fruit spots of stone fruits, was investigated in order to achieve a deeper insight in this taxon, thus enabling an improvement of the current diagnostic protocols and a more effective control of the disease. We confirmed the homogeneity of a vast collection of strains (over 100), isolated from stone fruit orchards during the last decade in Romagna (Northern Italy). Protein profiling and repPCR genetic fingerprints showed no significant differences among the strains: population homogeneity was also confirmed by phylotyping analysis. Copper resistant strains are present, but not widespread among the whole population. Xap is regulated (Directive 2000/29/EC, Annex A, Part II, Section II) and is included in the EPPO A2 list. An effective control of it is based both on analysis of propagation material and use of appropriate control strategies in the field. Based on available DNA sequences, we designed primers and attempted to developed a PCR protocol to be used in certification schemes. We also conducted field and glasshouse trials on peach, with the aim to effectively control the disease by using novel molecules, such as Glucohumates or antagonistic bacteria. Results are very promising and suggest the possibility to implement effective control strategies, where copper compounds and novel molecules are both used in commercial orchards.