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Understanding countrywide pathogen population structure and inter‐epidemic region spread is crucial for deciphering crop potential losses. Wheat stripe rust caused by Puccinia striiformis f. sp. tritici is a destructive disease that affects worldwide wheat production, widespread in China, representing largest epidemic region globally. This study aimed to understand the population structure and migration route of P. striiformis f. sp. tritici across China based on sampling from 15 provinces representing six epidemic zones, viz., over‐summering, over‐wintering, eastern, Yun‐Gui, Xinjiang and Tibet epidemic regions. High genotypic diversity was recorded in over‐summering, Tibet and over‐wintering epidemic regions. Epidemic regions partly explain population subdivision with variable divergence (FST = 0.005–0.344). Xinjiang and Tibet epidemic regions were independent epidemic zones with least sharing of genotypes. Among other epidemic zones, i.e. over‐summering, over‐wintering, eastern and Yun‐Gui epidemic zones, re‐sampling MLGs, clustering‐based structure, DAPC analyses, relative migration and low divergence (FST from 0.006 to 0.073) revealed frequent geneflow. Yun‐Gui epidemic regions, with a potential for both over‐summering and over‐wintering, could play an important role in causing epidemics in main wheat‐cultivating areas of China. High diversity, recombination signatures and inter‐epidemic region migration patterns need to be considered in host‐resistant cultivar development in China and neighbouring countries, considering risk of long‐distance migration capacity of pathogen.