Abstract: This study aims to solve the problem of distinguishing wheat varieties. 160 main cultivated wheat varieties were taken as experimental materials from Huang-Huai-Hai region and the middle-to-lower reaches of the Yangtze River, 21 pairs of stable and high polymorphism primers on each chromosome were screened from 21 linkage groups distributed in 105 pairs of SSR primers as SSR fluorescence based on capillaryelectrophoresis analysis. The authors constructed the wheat variety fingerprints and digitally encoded molecular ID of 160 wheat varieties combining with the varieties’basic commodity information. The results realize the unity of the uniqueness, universality, identifiability and traceability of wheat varieties’information, which provide convenience for the quality tracing and management of wheat seeds and scientific evidence for the protection of intellectual property right.