To test the hypothesis that copepods are able to regulate their buoyancy via altering their ionic content, we analyzed both the cation concentration in the hemolymph of Antarctic pelagic copepod species in late winter and the vertical distribution pattern and population structure. High concentrations of ammonia/ammonium (NH3/NH+4) were measured only in the hemolymph of Calanoides acutus, an Antarctic copepod definitely known to undergo vertical ontogenetic migrations and diapause at great depth, and in Rhincalanus gigas, in which a vertical ontogenetic migration pattern associated with diapause is still under debate. None of the other investigated species showed elevated ammonium concentrations in their hemolymph. We suggest that ion replacement by ammonium contributes to neutral buoyancy in diapausing calanoid copepods in the Southern Ocean. We hypothesize that ammonium buoyancy changes with season and is associated with shifts in extracellular pH and, therefore, most likely mediates metabolic depression during diapause. © 2010, by the American Society of Limnology and Oceanography, Inc.