Wheat leaf rust is a fungal disease caused by Puccinia triticina and spread by wind. In recent years, with changes in the climate and farming systems, damage caused by wheat leaf rust has become increasingly severe. To study the genetic structure of P. triticina populations in China and provide a basis for control of wheat leaf rust, collections of P. triticina were obtained from Xinjiang, Inner Mongolia, Hebei, Henan, Jiangsu, Anhui, Hubei, Sichuan, Guizhou and Yunnan provinces in 2019. A total of 177 single uredinial isolates were tested with 13 simple‐sequence repeat (SSR) primers. The results showed that there was frequent gene exchange within P. triticina populations in China, but a distinct population divergence was also revealed between those in Xinjiang and Yunnan provinces. Results also suggested that Inner Mongolia might be a source of P. triticina for other regions. In addition, the linkage disequilibrium test indicated that the P. triticina populations reproduced by clonal production of urediniospores. [ABSTRACT FROM AUTHOR]