Summary Allorecognition, the ability to discriminate between self and non-self, is ubiquitous amongst colonial metazoans and widespread amongst aclonal taxa [1–3]. Genetic models for the study of allorecognition have been developed in the jawed vertebrates [4], invertebrate chordate Botryllus [5, 6], and cnidarian Hydractinia [7]. In Botryllus, two genes contribute to the histocompatibility response, FuHC [5, 8] and fester [6]. In the cnidarian Hydractinia, one of the two known allorecognition loci, alr2, has been isolated [7] and a second linked locus, alr1, has been mapped to the same chromosomal region, called the allorecognition complex (ARC) [9, 10]. Here we isolate alr1 by positional cloning and report it to encode a transmembrane receptor protein with two hypervariable extracellular regions similar to immunoglobulin (Ig)-like domains. Variation in the extracellular domain largely predicts fusibility within and between laboratory strains and wild-type isolates. Alr1 was found embedded in a family of immunoglobulin superfamily-like (IgSF) genes, thus establishing that the ARC histocompatibility complex is an invertebrate IgSF-like gene complex.