AbstractInferring the dispersal processes of vector-borne plant pathogens is a great challenge because the plausible epidemiological scenarios often involve complex spread patterns at multiple scales. The spatial genetic structure of ‘CandidatusPhytoplasma prunorum’, responsible for European stone fruit yellows disease, was investigated by the application of a combination of statistical approaches to genotype data of the pathogen sampled from cultivated and wild compartments in three FrenchPrunus-growing regions. This work revealed that the prevalence of the different genotypes is highly uneven both between regions and compartments. In addition, we identified a significant clustering of similar genotypes within a radius of 50 km or less, but not between nearby wild and cultivatedPrunus. We also provide evidence that infected plants are transferred between production areas, and that both species of theCacopsylla prunicomplex can spread the pathogen. Altogether, this work supports a main epidemiological scenario where ‘Ca. P. prunorum’ is endemic in — and generally acquired from — wildPrunusby its immature psyllid vectors. The latter then migrate to shelter plants that epidemiologically connect sites less than 50 km apart by later providing infectious mature psyllids to their “migration basins”. Such multi-scale studies could be useful for other pathosystems.