Blue crab, Callinectes sapidus Rathbun, megalopae settle in seagrass or other complex submerged aquatic habitats in estuaries, where they metamorphose to the first juvenile (J1) crab stage. Within tidal areas, early juveniles (J1–2) leave such nursery areas by undergoing secondary dispersal during nocturnal flood tides. The present study determined whether J1–2 blue crabs have a biological rhythm in vertical swimming activity that contributes to secondary dispersal. Endogenous rhythms in vertical swimming were determined for (1) J1–2 crabs collected from two estuaries with semi-diurnal tides, (2) J1 crabs that metamorphosed from the megalopal stage in the laboratory the day after collection, and (3) premolt megalopae that metamorphosed to J1 crabs under constant conditions during the experiment. In all cases, a circadian rhythm was present in which crabs swam vertically during the time of night in the field. The time of peak vertical swimming did not correspond to the time of flood tide at the collection sites, but did consistently occur at night, with a mean around midnight. While responses to environmental factors probably control the onset and end of vertical swimming by early juvenile blue crabs during flood tides in tidal areas, a circadian rhythm underlies secondary dispersal at night.