Abstract: Super enhancers (SEs) are extraordinary long clusters of transcriptional enhancers formed by consecutive control units in series. They manipulate the of relevant genes. Hundreds of SEs in cells control key genes and determine the destiny of cells. Recent studies show that the of pathogenic genes, causing malignancies, Alzheimer’s disease, diabetes and many autoimmune diseases, is highly related to the aberrant activation of SEs. In this paper, we firstly outline the discovery and research development on SEs, illustrating methods to identify SEs, and then introduce databases related to SEs. We summarize the recent progress of SEs involving in embryonic stem cells, malignancies tumor and immune-related diseases, followed by the future applications in clinical treatments of gynecological diseases.