ABSTRACT There have been numerous treatments of specific topics in speciation, but surprisingly few papers have compared patterns and processes of speciation across different organismal groups. In this review, we partially address this gap by asking how variation in genome architecture impacts speciation across the plant and animal kingdoms. First, we briefly summarise 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 may 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) a higher frequency of whole‐genome duplications (WGDs) and more rapid loss of synteny in plants; (2) a higher incidence and greater divergence of sex chromosomes in animals; (3) greater rates of sequence change, but slower rates of structural evolution, in animal relative to plant mitochondrial genomes; and (4) an often higher abundance of transposable elements (TEs) in plant genomes. Overall, we find the genomes of plants diverge much more rapidly in structure than those of animals (although there are many exceptions), perhaps contributing to a more rapid emergence of barriers to gene flow in plants. However, we also found that comparisons of genome evolution between the kingdoms are hampered by inconsistency in the methods employed, as well as 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 generalisations, it enables powerful comparative analyses that link differences in genome architecture to patterns and processes of speciation.