Laboratory studies on chimeras ofthe tunicate Botryllus schlosseri revealed the phenomenon of "allogeneic resorption" or "colony resorption," the elimination of one partner in a chimera. A hypothesis outlining the genetic basis of the resorption phenomenon is presented here. It proposes that allogeneic resorption in Botryllus is controlled by a polymorphic, ladder-like, tri-level hierarchial system of histocompatibility loci, with codominantly expressed alleles. The relative state of homozygosity at these alleles within each level reflects the state of the hierarchy in the resorption phenomenon. The Fu/HC haplotype of the tunicates serves as the first level, whereas the other two levels are each controlled by specific resorption alleles (Re/HC) that operate only after a response has failed to occur at previous levels. Some morphologically expressed similarities to murine minor histocompatibility loci (Hh-1 and Mls) are discussed.