Selection of settlement sites by planktonic larvae can have important impacts on adult population distributions. Three species of fiddler crabs - Uca pugilator, U. pugnax, and U. minax - commonly co-occur in mid-Atlantic estuaries of the USA. They share a common larval life history of export to coastal waters followed by reinvasion of the estuary as postlarvae (megalopae), but their adults occupy different habitats separated by salinity and sediment type. This separation of adults could be caused by differential larval supply, selective settlement, or by post-settlement processes. We examined the species composition of planktonic postlarvae delivered to an intertidal site with a monospecific population of U. pugilator and compared it to newly settled postlarvae and first-instar crabs at this site using a new multiplex PCR technique for species identification. We found that all 3 species were present in the plankton but that almost all settled megalopae were U. pugilator, indicating that selective settlement is important for maintaining the adult population distribution at this site. In addition, all first-instar crabs were U. pugilator except for a single U. pugnax individual, indicating that megalopae that initially settle in an inappropriate habitat can leave before metamorphosis. The multiplex PCR is faster and less expensive than existing molecular methods for identifying fiddler crab larvae and juveniles to species. Future experiments should examine the behavioral bases for the selective settlement of Uca spp. megalopae.