Abstract: With the rapid development of sequencing technology and bioinformatics, hundreds of plant reference genomes have been sequenced, which has greatly promoted the development of plant functional genomics, evolutionary genetics, and molecular breeding. However, increasing evidence suggests that one reference from a single individual is insufficient to comprehensively understand the genetic diversity of a given species. The pan-genome concept has been proposed and successfully employed in studies of more than 20 plant species, uncovering abundant novel genes and genetic variations and deepening our understanding of genetic diversity. Here, we briefly introduce the concept and construction of pan-genomes, as well as their applications, development, and prospects in plant research.