Allorecognition--the ability of an individual to distinguish between self and non-self cells and tissues--ultimately depends on the presence of highly polymorphic gene(s). Allorecognition loci are the most diverse ever described, with tens to hundreds of alleles observed in a population. An unresolved problem in population genetics lies in understanding the origins, accumulation and maintenance of this extensive polymorphism, often over millions of years and across multiple speciation events. Botryllus schlosseri, a primitive chordate, has a life history that links several components of allorecognition from disparate fields that are experimentally accessible. This review outlines these traits and discusses some of the puzzling aspects of allorecognition in Botryllus that might contribute to understanding the evolution of these extraordinary polymorphisms.