In botryllids (colonial ascidians), there are two types of allorecognition: colony specificity and colony resorption. Colony specificity is manifested by fusion and rejection between two conspecific colonies. The genetic basis for this colony specificity resides in a single highly polymorphic gene locus (fusibility locus) with codominantly expressed alleles. Two colonies with no alleles in common at this locus reject each other, whereas colonies sharing at least one allele at the fusibility locus fuse and form a chimera. That is, in colony specificity, self components are distinguished from nonself components, and failure to recognize self induces rapid rejection reactions. The process of rejection in colony specificity is not uniform among all botryllid ascidians. Colony resorption can occur after the establishment of fusion between two colonies. Zooids of one partner of a chimera are resorbed more than 1 week after fusion, or, by amputation of fused blood vessels, the chimera becomes separated into the two original colonies. Colony resorption is also controlled mainly by the fusibility locus. It usually occurs in a chimera between two colonies sharing only one allele at this locus. In colony resorption, nonself determinants are recognized and chronic rejection reactions are induced resembling MHC-dependent graft rejection. Based on these findings, the fusibility locus of botryllids seems to be very similar to the MHC of vertebrates. Considering that vertebrates evolved directly from ascidians, it is likely that the fusibility locus is an ancestral form of the vertebrate MHC.