Continuing advances in genome sequencing technologies and computational methods for comparative genomics currently allows inferring the evolutionary history of entire plant and animal genomes. Based on the comparison of the plant and animal genome paleohistory, major differences are unveiled in (i) evolutionary mechanisms (i.e. polyploidization vs. diploidization processes), (ii) genome conservation (i.e. coding vs. non-coding sequence maintenance), and (iii) modern genome architecture (i.e. genome organization including repeats expansion vs. contraction phenomena). This article discusses how extant animal and plant genomes are the result of inherently different rates and modes of genome evolution resulting in relatively stable animal and much more dynamic and plastic plant genomes.