Nearly half of the genera of the family Caligidae possess an evolutionarily novel structure called the “lunule” on the ventral surface of the frontal plate. Lunules are paired cup-like suckers that assist in securing attachment of the copepod parasite to its host. Although present in genera such as Caligus and Pseudocaligus, lunules are absent in other caligid genera such as Lepeophtheirus as well as in more primitive caligiforms such as members of the families Trebiidae and Dissonidae. We compared the morphology and development of the anterior margin of the frontal plates between two caligids, Pseudocaligus fugu and Lepeophtheirus sekii, and a more basal caligiform, Dissonus heronensis (a dissonid), using scanning electron, transmission electron, and laser confocal microscopes. Our observations suggest that the lunules originated as a modification of the marginal membranes of the ancestral frontal plates. We also demonstrated the presence of an anlagen cell population for the lunule and marginal membrane in the developing frontal plate. These primordial cells can be detected as early as the first stage of the chalimus phase. Based on these observations, an evolutionary scenario for the lunule is proposed based on cytological evidence. This case study enhances our understanding of “evolutionary novelty,” which is a main focus of contemporary evolutionary developmental biology.