Self-incompatibility (SI) systems are common genetic systems in flowering plants that enforce outcrossing in hermaphrodite plants through several distinct pollen-pistil self-recognition molecular mechanisms. Although those molecular mechanisms have been deciphered in only a handful of flowering plants families, their diversity is particularly striking. One key to this diversity is that SI systems evolved many times independently in divergent plant lineages. However, recent studies have revealed that those molecular mechanisms can also vary among more closely related lineages, such as within a given plant family like the Brassicaceae or Rosaceae. We hypothesize that whole genome duplications (WGD) occurring within lineages may impact greatly the distribution and diversity of SI systems, especially when associated with allopolyploidy that generates strong genetic bottlenecks. Taking advantage of our detailed knowledge on the Brassicaceae SI system, and of the frequent occurrence of WGD events within this family, we investigated the relationship between WGD and diversity of genes involved in SI within the Brassicaceae family.