In the last decades, the population structure of some plant pathogenic bacteria has been assessed by using neutral markers. However, the dynamics of such populations as well as host plant and environment selection, gene flow and genetic drift have been analysed to a lesser extent. Insights into the sequential adaptation occurring between the crop and the micro-organism can also contribute to achieve a more effective control of the disease in the long run. In this review the possible centre of origin, often in relation to the geographic history of the crop, is discussed for some phytopathogenic bacteria, such as Xanthomonas axonopodis pv. citri, Xanthomonas axonopodis pv. cassavae, Xanthomonas oryzae pv. oryzae, Erwinia amylovora and Xylella fastidiosa. The rapid genetic change of bacteria through lateral gene flow and the efficient exploration of new adaptive solutions by exploiting the "contingency genes" of mutator clones, might also explain the occurrence of new diseases. Host selection, changes in environmental conditions and the introduction of new agronomic techniques, can play an important role in structuring the bacterial populations and in dramatically altering the equilibrium between the host plant and the pathogen. The prediction of such disturbances of equilibrium is fundamental for disease management.