<p>Sainfoin (<i>Onobrychis viciifolia</i>) is a significant leguminous plant recognized for its drought and salt tolerance, as well as its nitrogen-fixing capabilities. It has widespread applications in forage crops and ecological restoration due to its high nutritional value, particularly its tannin and proanthocyanidin (PA) content, which improves ruminant digestion and reduces parasite infection. However, research into the genetic diversity of sainfoin remains limited. Existing studies employing molecular markers like RAPD and ISSR have uncovered considerable genetic diversity among different sainfoin varieties, which is essential for future breeding work. Research progress on its genome and transcriptome, as well as the identification of genes related to stress tolerance, could further enhance molecular breeding techniques. Sainfoin’s extensive genetic diversity offers substantial potential for breeding stress-resistant and nutritionally superior varieties. This review discusses the genetic diversity, genomics, transcriptomics, and stress tolerance mechanisms of sainfoin, as well as its secondary metabolites, evaluating its potential in modern agriculture and ecological applications. The findings pave the way for future research and breeding efforts, aiming to optimize the use of sainfoin in both agriculture and ecosystem restoration.</p>