The dissemination of stolbur phytoplasma (16Sr-XIIA group)-induced yellows diseases depends on the dispersal biology and host plant fidelity of the planthopper vector Hyalesthes obsoletus (Hemiptera: Cixiidae). We analysed the degree of these two properties in H. obsoletus by studying its population genetic structure and stolbur infection rates relative to the two major host plants, Convolvolus arvensis and Urtica dioica, in order to infer relevant divisions for stolbur epidemiology in Swiss viticultural regions. Three regional populations with the potential to determine stolbur epidemiology in distinct ways were identified. First, populations associated with U. dioica in northern Switzerland were most related to genetically distinct U. dioica host race populations identified previously in Germany. Second, populations in central and southwest Switzerland were undifferentiated relative to host plant and likely have wider stolbur transmission breadths than the northern specialized populations. Third, populations in south of the Alps (Ticino) were undifferentiated relative to host plant but geographically isolated from other Swiss regions, thus implying separate population dynamics in this area. The knowledge of these three distinct epidemiological cycles will help to adapt management programmes against stolbur diseases in Swiss vineyards.