Foxtail millet was one of the important positions in grain crops. With the completion of its whole genome sequencing, it had greatly promoted the development of molecular markers of foxtail millet. As the second generation, with a simple operation, good reproducibility and reliable results and other advantages, SSR markers technology had been widely adopted in crop genetic diversity, construction of genetic linkage map, analysis of quantity shape, species identification and other research. The application in genetic diversity and other research of SSR markers in foxtail millet were reviewed, and it was expected to provide information and reference for the development of SSR markers in foxtail millet.