Leaf rust of wheat caused by Puccinia triticina (Pt) is one of the most common and widespread fungal diseases which has a wide incidence area, especially in the southwest and northwest of China, the middle and lower reaches of the Yangtze river, and the southern part of the Huang-huai-hai river basin. To explore the relationship between the epidemic flora of leaf rust and transmission, a total of 709 isolates from Beijing, Hebei, Henan, Shandong, Shanxi, Shaanxi, Anhui, Jiangsu, Hubei, Yunnan, Sichuan, Gansu, Qinghai, Heilongjiang, Inner Mongolia 15 provinces was genotyped using 13 simple sequence repeat (SSR) markers. The Puccinia triticina populations from the 15 provinces were obviously divided into three predominant populations including the eastern Pt populations consisting of Pt samples from eight eastern provinces of Beijing, Hebei, Shandong, Anhui, Henan, Shanxi, Shaanxi and Heilongjiang; the four western Pt populations from Gansu, Sichuan, Qinghai and Inner Mongolia provinces; and the bridge Pt populations including Pt samples from Jiangsu, Hubei and Yunnan provinces which were communicated with the other two populations as a “bridge”. And the pathogen source transmission of eastern Pt populations was more frequent than western Pt populations. The linkage disequilibrium test indicated that the whole Pt population was linkage disequilibrium. Beijing, Hebei, Shaanxi, Jiangsu, Henan and Heilongjiang provinces were showed obviously linkage equilibrium phenomena while the five provinces of Qinghai, Hubei, Anhui, Shandong and Inner Mongolia were supported clonal mode of reproductions. In addition, provinces of Shanxi, Yunnan, Gansu, and Sichuan showed weak linkage disequilibrium phenomena. We systematically revealed the genotypic diversities, population differentiation and reproduction of P. triticina in 15 wheat producing areas in China.