Understanding of long-term virulence dynamics of pathogen populationsin response to host resistance gene deployment is of major importancefor disease management and evolutionary biology. We monitoredthe virulence dynamics of Puccinia striiformis f. sp. tritici, the causalagent of wheat stripe rust, over 25 years in France. Virulence dynamicswas explained by estimates of area associated with resistance genescarried by farmers' cultivars. The epidemics assessed through diseaseseverity significantly correlated with the number of P. striiformis f. sp.tritici isolates collected each year, used to describe virulence dynamics.In the south, the dominance of the Mediterranean pathotype 6E16and the cultivation of a susceptible cultivar were associated with anepidemic from 1997 to 1999. In the north, five epidemics occurred dueto successive acquisition of virulence to the resistance genes Yr7, Yr6,Yr9, Yr17, and Yr32, either by acquisition of the virulence in the previousdominant pathotype or by incursion or selection of one or two newpathotypes. Frequency of pathotypes with Vr7 and Vr6 declined withthe reduction in the cultivation of corresponding Yr gene cultivars,whereas the virulence Vr9 persisted longer than the cultivation of Yr9cultivars. Although the first pathotypes carrying Vr9 decreased, thisvirulence persisted in other pathotypes even in the absence of Yr9 cultivars.At the regional level, Yr9 cultivars in the north caused a shift fromhigh Vr6 frequency to high Vr9 frequency whereas, in the central region,where Yr9 cultivars were rare, Vr6 remained prevalent.