Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst) is an important wheat disease worldwide. In this study, the pathogen population in Canada representing a time period of 30 years since 1984, was analysed for virulence diversity, and geographical distribution, and was compared with previously described races from the main stripe rust regions in the United States. The virulence of 140 isolates of Pst was evaluated on 18 near-isogenic wheat lines in the Avocet background. The seedlings were inoculated with a spore/talc mixture (ratio 1:20) and infection types (ITs), on the second leaf, were evaluated 18–21 days after inoculation based on a scale of 0–9. In total, 89 different races were observed and grouped under 12 main virulence groups. Based on the virulence profile and the defeated Yr genes, a clear change in the pathogen virulence has been observed through time. Pst in Canada remains avirulent on Yr1, Yr5, and Yr15, but has high frequency of virulence on Yr6, Yr17, YrTr1, and YrExp2 since 1984. Pst virulence has spiked on Yr7 and defeated for first time Yr8 and Yr9 since 2000, and defeated Yr10 and Yr27 since 2010. Overall, the dominant races in Canada were very similar to the main races previously reported in USA (PSTv-41, PSTv-37, PSTv-52), which indicates a long-distance migration of these races from the United States to Canada. However, the presence of significant number of unique virulence patterns in Canada at low frequencies support the hypothesis of mutation of virulence/avirulence for host resistance in local regions. Analysis of diversity between isolates collected from Canadian provinces and the races collected from USA showed that the Pst population in Western Canada is similar to that in Western USA, and the Pst population in Eastern Canada is similar to that in eastern and/or central regions of USA. This supports the hypothesis that Pst in North America travels through different wind trajectories.