Pathogen populations are expected to evolve virulence traits in response to resistance deployed in agricultural settings. However, few temporal datasets have been available to characterize this process at the population level. Here, we examined two temporally separated populations ofPuccinia coronataf. sp.avenae(Pca), which causes crown rust disease in oat (Avena sativa) sampled from 1990 to 2015. We show that a substantial increase in virulence occurred from 1990 to 2015 and this was associated with a genetic differentiation between populations detected by genome-wide sequencing. We found strong evidence for genetic recombination in these populations, showing the importance of the alternate host in generating genotypic variation through sexual reproduction. However, asexual expansion of some clonal lineages was also observed within years. Genome-wide association analysis identified sevenAvrloci associated with virulence towards fifteenPcresistance genes in oat and suggests that some groups ofPcgenes recognize the same pathogen effectors. The temporal shift in virulence patterns in thePcapopulations between 1990 and 2015 is associated with changes in allele frequency in these genomic regions. Nucleotide diversity patterns at a singleAvrlocus corresponding toPc38,Pc39,Pc55,Pc63,Pc70, andPc71showed evidence of a selective sweep associated with the shift to virulence towards these resistance genes in all 2015 collected isolates.