Flowering plants have evolved through repeated ancient genome duplications (or paleo-polyploidies) for ~200 million years, a character distinct from other eukaryotic lineages. Paleo-duplicated genomes returned to diploid heredity by means of extensive sequence loss and rearrangement. Therefore repeated paleo-polyploidies have left multiple homeologs (paralogs produced in genome duplication) and complex networks of homeology in modern flowering plant genomes. In the first part of my research three paleo-polyploidy events are discussed. The Solanaceae T event was a hexaploidy making extant Solanaceae species rare as having derived from two successive paleo-hexaploidies. The Gossypium C event was the first paleo-(do)decaploidy identified. The sacred lotus (Nelumbo nucifera) was the first sequenced basal eudicot, which has a lineage-specific paleo-tetraploidy and one of the slowest lineage evolutionary rates. In the second part I describe a generalized method, GeDupMap, to simultaneously infer multiple paleo-polyploidy events on a phylogeny of multiple lineages. Based on such inferences the program systematically organizes homeologous regions between pairs of genomes into groups of orthologous regions, enabling synte-molecular analyses (molecular comparison on synteny backbone) and graph representation. Using 8 selected eudicot and monocot genomes I showed this framework of multiple paleo-polyploidy detection and synte-molecular network facilitates genomic comparisons among flowering plants and reveals deep correspondences among their genome structure.