Phytoplasmas are cell wall-less microorganisms belonging to the class Mollicutes, and are associated with plant diseases worldwide. Typically located in the plant phloem tissue, they are transmitted by sap-sucking insect vectors, and induce typical symptoms (Bertaccini and Duduk, 2009). On the basis of conserved 16S rRNA gene sequence similarity, the currently known phytoplasmas are classified into a number of different 16S ribosomal (16Sr) groups and subgroups (Duduk and Bertaccini, 2011; Dickinson et al., 2013). Many important food, vegetable and fruit crops can be severely affected by these pathogens with a significant economic impact (Bertaccini and Duduk, 2009). Flavescence dorée (FD) is one of the greatest threats for grapevine cultivation in Europe and included in European legislation as a quarantine pest (directive 2000/29 EC). It is caused by a phytoplasma belonging to 16SrV group, efficiently transmitted by the insect vector Scaphoideus titanus Ball. More recently some other leafhoppers have been shown to harbour FD phytoplasma: Dictyophara europaea (Filippin et al., 2009) and Orienthus ishidae (Gaffuri et al., 2011; Mehle et al., 2011). D. europaea was also demonstrated to trasmit FD from Clematis vitalba to grapevine (Filippin et al., 2009) Interest has recently been focused on several wild species, found infected by FD, to verify their possible role in FD epidemiology: Clematis vitalba, Alnus glutinosa (Malembic-Maher et al., 2009) and Ailanthus altissima (Filippin et al., 2010). Genetic analysis of FD genome with different molecular markers revealed a population variability and the presence of different FD strains in the 16S rDNA, belonging to subgroups 16SrV-C and 16SrV-D (Martini et al.,1999; Arnaud et al., 2007).