Understanding how novel structures arise is a central question in evolution. The carapace of the waterflea Daphnia is a bivalved cape of exoskeleton that has been proposed to be one of many novel arthropod structures that arose through repeated co-option of genes that also pattern insect wings. To determine whether the Daphnia carapace is a novel structure, we compare the expression of pannier, araucan, and vestigial between Daphnia, Parhyale, and Tribolium. Our results suggest that the Daphnia carapace did not arise by co-option, but instead derives from an ancestral exite (lateral lobe) that emerges from a proximal leg segment that was incorporated into the Daphnia body wall. The Daphnia carapace therefore appears to be homologous to the Parhyale tergal plate and the insect wing. Remarkably, the vestigial-positive region that gives rise to the Daphnia carapace appears to be present in Parhyale and Tribolium as a small, inconspicuous protrusion. Similarly, the vestigial-positive developmental fields that form tergal plates in Parhyale appear to be present in Daphnia, even though Daphnia does not form tergal plates. Thus, rather than a novel structure resulting from gene co-option, the Daphnia carapace appears to have arisen from a shared, ancestral developmental field that persists in a cryptic state in other arthropod lineages. Cryptic persistence of unrecognized serially homologous developmental fields may thus be a general solution for the origin of novel structures. Our simple molecular triangulation strategy, which does not require functional studies, can illuminate the homologies of long-debated structures on the legs and body wall of arthropods.