Nearly forty years ago, Susumu Ohno proposed that one or two rounds of whole genome duplication took place close to the origin of vertebrates. The refined version of this proposal, known as the two round (2R) hypothesis, assumes that the genome of jawed vertebrates has been shaped by two rounds of whole genome duplication that took place after the emergence of urochordates and before the radiation of jawed vertebrates. Although this hypothesis has been a focus of heated debate in recent years, it is increasingly supported by genome-wide analysis of key chordate species. The 2R hypothesis has important implications for understanding the evolution of the immune system, including the origin of the major histocompatibility complex and natural killer receptors.