Wheat stripe rust is an emerging pest problem in Canada and several epidemics in the past have spurred research on the causal pathogen (Puccinia striiformisf. sp. tritici- Pst) for disease management. To breed for resistance, it is imperative to understand the rust pathogen populations including race dynamics, genetic changes in the races/lineages, and effective resistance genes against prevalent races. Presently, >40 Pst races have been characterized from Canada. We have genotyped a large collection of Pst isolates collected from across Canada and sequenced (>30X coverage) some representative races. Our investigation of the genetic population structure (2009-2016) of the Canadian Pst population using molecular markers and genome re-sequencing, revealed the presence of four divergent lineages with predominantly clonal structure. From a global context, two previously reported lineages were identified: PstS0 (22%), representing an old Northwestern-European and PstS1 (35%), an invasive warm-temperature adapted. Additionally, two new, unreported lineages, PstPr (9%) and PstS1-related (35%), were detected, which produced more telia than other lineages and had double the number of unique recombination events. The PstPr was a recent invasion, and likely evolved in a diverse, recombinant population as it was closely related to the PstS5, PstS7/Warrior, PstS8/Kranich, and PstS9 lineages originating from sexually recombining populations in the centre of diversity. The 2016, the Pst population from western Canada belonged to the PstS1-related lineage. On the epigenetics side, DNA methylation analysis revealed DNAmethyltransferase1-homologs, providing compelling evidence for epigenetic regulation and as a first report, an average of ~5%, 5 hmC in the Puccinia epigenome merits further investigation. This presentation will summarize published and unpublished results from current studies on Pst in Canada as well as the ongoing work to elucidate structural variations among different race groups.