As a new branch of genomics, plant paleogenomics reconstructs ancestral genomes from actual modern species and infers palaeohistory, evolutionary and/or speciation events that have shaped the modern species. Advances in high-throughput sequencing technologies yield accurate long reads, promote the progress of plant genome sequence assembly, and thereby offer paleogenomics a large collection of valuable reference genomes from modern species. Whole-genome duplication (WGD) and polyploidization cause rapid genomic reorganization, massive gene losses and structural variations. WGD events are therefore central to plant evolution. In this review, we summarize recent progress in sequencing and assembly of plant genomes, principles of plant paleogenomics, WGD events in plant genomes, and the most likely evolutionary scenario in plants. Furthermore, we highlight some of the challenges as well as future directions.