Genetic diversity and population structure analysis of 171 wild and cultivated Psathyrostachys individual germplasms from different countries and regions were conducted by 38 pairs of SSR primers. The result by using the effective primers revealed a total of 308 loci among Psathyrostachys individuals, with 275 polymorphic loci and a polymorphism percentage of 89.29%. The genetic similarity coefficient of the tested materials ranged from 0.537 to 0.899 with an average of 0.742. These accessions were divided into three groups by population structure analysis, principal component analysis and NJ clustering. The genetic similarity coefficient analysis showed that the distribution of Psathyrostachys individuals was more concentrated. The classification using three methods generally revealed three different groups of Psathyrostachys materials, despite that there were slightly different in the divisions of mixed groups. Since these Psathyrostachys individuals in each group showed different on genetic background, no clear correlation between geographic distribution and genetic diversity was observed.