Rhamnose-binding lectins (RBLs) in vertebrates function in immunity as pattern recognition receptors, opsonization agents, and activators of pro-inflammatory cytokines. Although they have been identified in some invertebrate taxa, their distribution, function, and evolutionary patterns in basal metazoans, remain largely unknown. A unique RBL-containing protein composed of 8 thrombospondin type 1 repeats (TSRs) and a single RBL domain has been identified in the colonial hydroid Hydractinia symbiolongicarpus. This Rhamnospondin (Rsp) gene was specifically and constitutively expressed in the mouth of feeding polyps. Here we report the full characterization of a second Rsp gene from a H. symbiolongicarpus BAC library. Rsp1 and Rsp2 were 1.1kb apart, shared the same domain architecture and were 93% identical. Introns differed substantially in size and sequence, excepting two introns that were nearly identical, suggesting the action of inter-locus recombination. Sequencing full-length cDNAs from a wild-type individual corroborated the exon boundaries predicted from genomic DNA and showed gene polymorphism at both loci. Database searches and phylogenetic analyses showed that Rsp was found only in hydrozoans, indicating that it is an innovation of the cnidarian class Hydrozoa. Phylogenetic analysis of Rsp sequences in hydroids show a tendency of clustering paralogous genes, suggesting that they have evolved by concerted evolution.