Colonial basal metazoans often encounter members of their own species as they grow on hard substrata, with the encounters typically resulting in either fusion of close relatives or rejection between unrelated colonies. These allorecognition responses play a critical role in maintaining the genetic and physiological integrity of the colony. Allorecognition responses in basal metazoans are controlled by highly variable genetic systems. The molecular nature of such systems, however, remains to be determined. Current efforts to identify the genes and molecules controlling allorecognition in basal metazoans have followed two pathways: identification of molecules differentially expressed in incompatible interactions, and positional or map-based cloning of allorecognition genes. Most studies following the first approach have been performed with marine demosponges, while those following the second approach have centered on the cnidarian of the genus Hydractinia. Here, I discuss the latter, focusing primarily on the genetic control of allorecognition responses.