This dataset is related to the submitted paper " A single gene determines allorecognition in hydrozoan jellyfish Cladonema radiatum inbred lines ". Abstract: Allorecognition—the ability of an organism to discriminate between self and non-self—is crucial to colonial marine animals to avoid invasion by other individuals in the same habitat. The cnidarian hydroid Hydractinia has long been a major research model in studying invertebrate allorecognition, establishing a rich knowledge foundation. In this study, we introduce a new cnidarian model Cladonema radiatum (C. radiatum). C. radiatum is a hydroid jellyfish which also forms polyp colonies interconnected with stolons. Allorecognition responses, fusion or regression of stolons, are observed when stolons encounter each other. By transmission electron microscopy, we observe rapid tissue remodelling contributing to gastrovascular system connection in fusion. Rejection responses are regulated by reconstruction of the chitinous exoskeleton perisarc, and induction of necrotic and autophagic cellular responses at cells in contact with the opponent. Genetic analysis identifies allorecognition genes: six Alr genes located on the putative Allorecognition Complex (ARC) and four immunoglobulin superfamily genes on a separate genome region. C. radiatum allorecognition genes show notable conservation with the Hydractinia Alr family. Remarkedly, stolon encounter assays of inbred lines reveal that genotypes of Alr1 solely determine allorecognition outcomes in C. radiatum.