This review asks how variation in genome architecture impacts speciation across the plant and animal kingdoms. First, we briefly summarize what is known about speciation in these groups; importantly, the diversification rate of plants is about twice that of animals, and species barriers in plants appear to arise at an earlier stage of divergence. Next, we discuss several of the major differences in how plant and animal genomes evolve, and how they may impact the evolution of reproductive barriers and potentially speciation rates. Key differences include (1) the higher frequency of whole genome duplications and more rapid loss of synteny in plants; (2) the higher incidence and greater divergence of sex chromosomes in animals; (3) higher rates of sequence change, but slower rates of structural evolution, in animal relative to plant mitochondrial genomes; and (4) the higher abundance of transposable elements in plant genomes. Overall, we find the genomes of plants typically diverge much more rapidly in structure than those of animals (although there are many exceptions), which likely contributes to the more rapid emergence reproductive barriers in plants. However, we also found that comparisons of genome evolution between the kingdoms are hampered by inconsistency in the methods employed, and in the metrics used to report on rates of structural evolution. Another theme from our review is the huge variation in genome architecture within each kingdom. While this variation complicates broad generalizations, it also enables powerful comparative analyses that link differences in genome architecture to patterns and processes of speciation.