We have identified a novel, multidomain, polymorphic lectin in the marine cnidarian Hydractinia echinata. The gene is expressed in oocytes and was therefore named CEL for cnidarian egg lectin. The predicted protein has an unusual domain architecture, consisting of variable numbers of thrombospondin type 1 domains, flanked by one N-terminal and two C-terminal galactose binding lectin domains. The diversity of the gene's transcripts results from allelic polymorphism as well as alternative splicing. Hydractinia is dioecious and its sex has been reported previously to be genetically determined. We found intersexual colonies that were functional males, but had immature CEL-positive oocytes alongside mature sperm in the same gonads. Intersexuality was observed to be common in one population but not found in others. Hermaphroditic, self-fertile colonies were found in one locality; however, in these cases gonads contained either male or female gametes without mixed ones. Intersexuality that was considered to be a very rare event is apparently a more common phenomenon, at least in some populations. True hermaphroditism also occurs in this species. CEL can be considered as a marker for early oocyte differentiation and may play a role in germ cell specification and sex determination in cnidarians.