Rye is a cereal crop belonging to Genus Secale of the family of Gramineae with the Latin name as Secale cereale L., which is a staple ingredient in bread for European people, especially in the middle ages. But there is no strong evidence for the origin and phylogeny of rye. Recently, Bielefeld University, Germany, analyzed 726 samples from 139 cultivars of different cultivars, local varieties, weedy rye and wild rye populations from 45 different countries using single sequence repeat (SSRs) and the sequence diversity of nuclear expression sequence marker (EST) regions. The results showed that compared with the cultivated rye populations in other parts of the world, the cultivated rye populations in the Middle East had the highest genetic diversity, indicating that the Middle East in southwest Asia was the origin center of rye. The Secale species could be divided into three different clusters based on the STRUCTURE analysis of SSR loci.Based on UPGMA tree analysis, s. strictum was found to be the ancestor of Secale species.It is obvious that the origin and phylogeny of rye have achieved stage results.