Male “clam shrimps” possess highly modified first (and second) trunk limbs for clasping the carapace of females during copulation. Claspers are present in all three clam shrimp taxa (Laevicaudata, Spinicaudata, and Cyclestherida) but despite striking similarities in their morphology and function, the matter of their homology is controversial. In this study, we address the question of the homology and evolution of these structures by comparing the developmental transformation of an unspecialized trunk limb into a clasper. In addition, we study the musculature and the nervous system in trunk limbs and claspers using confocal laser scanning microscopy. We establish that most (but not all) of the various parts of the claspers are homologous between clam shrimp taxa. We suggest that a single pair of claspers was already present in the ground pattern of Diplostraca, probably most comparable to those in Cyclestherida. The claspers, therefore, do not represent a case of analogy. J. Exp. Zool. (Mol. Dev. Evol.) 322B: 269–280, 2014. © 2014 Wiley Periodicals, Inc.