Puccinia striiformis f. sp. tritici is a responsible pathogen for wheat stripe rust, which can be dispersed for a long distance by upper air flow. Understanding its origin and migration is vital to control the disease. We analyzed the population structures of the pathogen, which include 297 samples from Yunnan, Guizhou, Sichuan, Shaanxi, and Gansu in 2008 and 2011, by using the concatenated gene Cdc2-(Ef-1α)-Mapk1. From which, 18 vs 27 SNP loci, and 26 vs 23 haplotypes were tested in 2008 and 2011, respectively. The ancestral haplotype was detected in Yunnan in both years. Yunnan population had a higher mutation rate than Gansu population, which was 3.46e-03 vs 2.33e-03 in 2008, and 5.74e-03 vs 3.54e-03 in 2011, respectively. While the Gansu population had more recombination events than the Yunnan population, which was 3 vs 2 in 2008, and 5 vs 1 in 2011, respectively. The Gansu population had a higher genetic diversity than the Yunnan population, with the haplotype diversity of 0.7641 vs 0.7076 in 2008, and 0.8103 vs 0.4764 in 2011, respectively. There was a massive gene flow between Yunnan and Gansu, the Nm was 142.60 vs 9.47 in 2008 and 2011, respectively. The trajectories of upper air flow during wheat growing season from 2005 to 2013, directed mainly from Yunnan to Gansu. Based on above and previous researches regarding South Gansu as the crucial over-summering source of the stripe rust pathogen in China, Yunnan is suggested as the probable origin center for the pathogen in China, while Gansu is argued as the secondary center.