Super-enhancers (SEs) are large clusters of transcriptional enhancers that drive expression of genes controlling cell identity. They play important roles in development, disease initiation and progression such as tumorigenesis. Compared to typical enhancers (TEs), most key oncogenes in tumor cells are driven by SEs, and common diseases such as Alzheimer’s disease related variations are enriched in SEs. SEs hold great promising in key oncogenes identification and diseases-associated variants discovery. In this review, we first summarize how to identify enhancers on a genome-wide scale, and then introduce the concept of SEs and the methodology for SEs identification. Lastly, we describe SEs’ main structural and functional properties and discuss its application in the future research.