The flowering plants, also known as the angiosperms, are the most diverse group of plants. The basal flowering plant lineages diverged at very early stage in flowering plant evolution, followed by rapid diversification of the magnoliids, the eudicots and the monocots. Genomic comparisons within and across plant lineages help identify the critical events that occurred during the evolution of major groups of flowering plants. In this chapter, we first review the basic concepts and analytic methods for studying ancient polyploidy-a prominent feature during plant evolution. We then highlight recent progress on the dating of deep polyploidies in the eudicot and monocot lineage, respectively. With a clear knowledge of genomic history, we can effectively compare the eudicot genomes to monocot genomes, which promise to bridge functional equivalence between genes of the two well-studied groups. Finally, we deduce the composition and structure of the 'ancestral genome' on the basis of the arrangements of genes in the extant species. The in silico reconstruction of the ancestral genome provides an integrated framework under which conservation of modern plant genomes can be systematically studied.