Abstract: In this paper, the research progress of crop variety identification by four dominating molecular markers, AFLP, ISSR, SRAP and SSR, was summarized. It was proposed that the SSR should be the first choice in future when molecular markers were used to identify the purity of variety and test for DUS. Meanwhile, the research progress of rapid identification of the purity of variety was introduced. And it was predicted that the internet technology would be used in future to combine the fingerprinting of molecular markers and the morphological feature of crop varieties to obtain a quick index of varieties. The rapid identification of varieties would be also achieved through the alignment of digital fingerprinting between different varieties and the rapid output of information. The goal of rapid identification of the purity of varieties and authenticity in any growing period of crop would be realized, which would promote the protection for varieties of plants and the healthy development of China's seed industry.