The isolates of wheat stripe rust disease were collected in the year of 2004, 2012, 2014 and 2015 during the main wheat growing season February to May from ten counties of Yunnan province in China. The results from single nucleotide polymorphisms (SNPs) of 168 isolates showed that two housekeeping genes namely Citrate Synthase (CS) and heat shock protein 90kDa (HSP) were found to contain a total of 11 SNP sites. A total of 34 haplotypes were inferred from the concatenated sequences, with three haplotypes (H23, H32 and H16) comprising of over 40.5% of population and were shared haplotypes the population of Dehong, Yuxi, Lincang, Qujing and other counties. The haplotype diversity, nucleotide diversity, mutation rate and recombination events were 0.930, 4.46E-03, 4.46E-03 and 4 respectively, which revealed virulent diversity of Pst populations among all locations. All the three grouping methods (UPGMA-tree, PCA and Structure) used in the current study to classify the Pst populations according to their races and geographical locations, were found meaningful and most of the groups were co-linear in all the grouping methods. Using analysis of molecular variance (AMOVA), we found 6.13% of the total variation was among populations and 86.63% within populations. This revealed a relatively high genetic diversity came from inside population but low genetic divergence came from among populations. Moreover, the molecular data on gene flow (Nm=6.09) confirmed the migration of pathogen populations occurred among all locations in Yunnan Province. The ancestral haplotype (H25) detected in Zhaotong, Yuxi, Lincang, Chuxiong and Kunming and the other results also indicated that the frequent pathogen exchange within the locations. We analyzed the population structure in different locations of Yunnan intensively. Based on trajectories of upper airflow and genetic diversity of Pst populations in different locations, we suggested that Lincang, Dehong and Dali are probably source of Pst in Yunnan.