•We discuss the phenomenon of allorecognition in context of the evolution of immunity in the metazoa.•Recent findings on allorecognition in the colonial ascidian, Botryllus schlosseri are reviewed.•Potential models for allo-specificity in B. schlosseri are presented. Allorecognition has been well-studied in the context of vertebrate adaptive immunity and recognition of the Major Histocompatibility Complex (MHC), which is the central event of vertebrate immune responses. Although allorecognition systems have been identified throughout the metazoa, recent results have shown that there is no apparent conservation or orthologous relationship between the mechanisms underlying this phenomenon in different organisms. Thus the origin of the vertebrate adaptive immune system as well as these other complex recognition systems is a complete mystery. This review will focus on allorecognition in Botryllus schlosseri, a basal chordate which undergoes a natural transplantation reaction following contact between two individuals, and, analogous to vertebrates, is controlled by a single locus. We will summarize each of the known candidate genes within this locus and their potential roles in allorecognition, and speculate on how these findings may in fact be revealing potential functional relationships between disparate allorecognition systems.