Foxtail millet (Setaria italica) is cultivated in northern China dry land and semi-dry land area as staple grain, and its cultivation and domestication have a long history. Germplasm resources are the important basis of foxtail millet biology research and breeding improvement. China is regarded as the center of origin of foxtail millet and has abundant germplasm resources. Studies on genetic diversity of foxtail millet from different geographical origins have received remarkably progress worldwide. This paper reviews the research progress of foxtail millet germplasm resources: the research on the phenotype characteristic and quality traits diversity of foxtail millet, makes an overview of foxtail millet genetic diversity based on nutrition ingredient and biochemical marker analysis, and summarizes the main methods and achievements of foxtail millet germplasm diversity at DNA level. This paper not only provides a reference for future comprehensive and systematic research on millet genetic diversity, but also supplies useful information for the utilization of germplasm resources and millet breeding improvement in the future.