Pathogen migration is a source of new pathogens and pathotypes to a particular region. Studies on origin and migration of pathogens were difficult in the past, but DNA sequence data and new analytical approaches now enable us to analyze population genetic structures from which we can determine possible migration routes. The Himalayan and neighboring regions (Gansu, China) were earlier suggested as putative centers of origin for Puccinia striiformis f. sp. tritici (Pst) and sampling locations for Chinese isolates were strongly focused in South Gansu. Previous field surveys indicated that Yunnan might be the primary source of the Gansu population in China. Using samples collected in 2008 and 2011 we compared the Pst population structures of Yunnan and south Gansu for SNPs in housekeeping genes Cdc2, Ef-1? and Mapk1, and the trajectories of upper air flow during wheat growing seasons from 2005 to 2013. The ancestral haplotype was detected in the Yunnan population, which had higher a mutation rate than the Gansu population, but the latter contained more recombination events. Both populations were highly diverse. There was massive air flow between Yunnan and Gansu with trajectories being mainly from Yunnan to Gansu. We propose a putative dispersal route of Pst from Yunnan to South Gansu, making Yunnan the center of origin for Pst in China, whereas Gansu is a secondary center of origin. It is proposed that Pst migrates from South Asia to Yunnan under the influence of westerly weather patterns, and subsequently spreads to other parts in China. DNA sequence comparisons should be undertaken to compare Pst populations of South Asia and China in order to confirm these hypotheses.