Ischemic stroke is a multifactorial, heterogeneous cerebrovascular disease characterized by high incidence, mortality, disability, and recurrence rates. Currently, computed tomography or magnetic resonance imaging represents the gold standard for diagnosis and guidance of thrombolysis or thrombectomy. However, it has limitations such as the inability to provide rapid detection, distinguish etiologies, perform risk stratification, or enable dynamic monitoring. Therefore, rapid, convenient, and highly sensitive biomarkers hold significant clinical value. In recent years, rapid advancements in genetics and multi-omics technologies have not only driven the discovery of ischemic stroke biomarkers and the elucidation of pathophysiological mechanisms but also demonstrated broad application prospects in clinical translation-covering etiological subtyping, individual risk stratification and screening of high-risk populations, drug target identification, recurrence prediction, and prognostic assessment. These advances have laid a molecular foundation for achieving precise diagnosis and personalized treatment of ischemic stroke. This review summarizes biomarkers for ischemic stroke identified through genome-wide association study and multi-omics technologies. We also discuss the implications of these findings for the biological mechanisms of ischemic stroke and their clinical applications.