Eudicot plants comprise about 75% of angiosperm (flowering plant) species. They have inhabited much of the Earth since the Cretaceous period and include rich diversity of life forms and characters, many of which have contributed to sustaining human civilization. Genome sequences from over 35 eudicot species have been published since 2000, providing a basis for clarifying the relationships among eudicots and making inferences about their common ancestor. All eudicot lineages have been affected by paleopolyploidies (ancient genome duplications), a major evolutionary force that is prevalent in plants, and which obscures structural correspondences between genomes. Complicated paralogy patterns resulting from recurring genome duplications and rearrangements nullify straightforward one-to-one correspondence between genomes, necessitating accurate and sensitive synteny (conserved gene order) detection. Development of such computational algorithms led to discoveries of paleopolyploidy events in all sequenced eudicot genomes. In particular, simultaneous alignment of multiple related regions via 'top-down' approaches recovers cryptic synteny by making use of transitive homeology, enabling deep comparisons of distantly related genomes despite extensive structural rearrangements. Paleohexaploidy (ancient genome triplication) seems to be a phenomenon particularly influential in eudicot plants, including one such event that occurred in the eudicot stem lineage, preceding the diversification of core eudicots. At the end of this chapter, we review recent research towards reconstructing the eudicot ancestral genome. Systematic genome comparisons promise better understanding and utilization of structural and functional correlations in eudicots and other groups.