A survey was conducted over several years in Italy and the Balkans in order to gain an understanding of the relationship between the Flavescence dorée (FD) phytoplasma isolates found in clematis and grapevine. A total of 399 clematis and 107 grapevine samples were analyzed. The results showed that 36% of the Clematis vitalba plant samples were infected by phytoplasmas which, in grapevine, are associated with FD, a quarantine disease in Europe. Infected clematis plants were also found in areas where FD phytoplasma had never previously been reported to infect grapevine, such as Macedonia, Croatia and some areas of Italy and Serbia. Molecular data from three phytoplasma genomic fragments showed the presence of different FD phytoplasma isolates, all belonging to the 16SrV-C subgroup, including the Italian FD-C isolate, the isolate found in Serbia, an isolate similar to the French FD2000 and a new isolate typical of central Italy. A few clematis plants were infected with single nucleotide polymorphism, insertion or deletion mutants of the FD-C isolate. Of all the potential Hemipteran vector species surveyed in Italy and Serbia, only 18 of 527 Dictyophara europaea individuals tested proved to be infected with the FD phytoplasma. Preliminary transmission experiments showed that this species is able to transmit the FD phytoplasma from clematis to grapevine. The presence of FD-infected clematis and of D. europaea could, therefore, constitute a risk for FD epidemics in the European viticultural regions.