Among Anoplura, the family Echinophthiriidae includes species that infest pinnipeds and otters. Previous evidence obtained from pinnipeds infested by echinophthiriids, specifically from seals, indicates that flippers are the preferred infestation sites, while lice from fur seals select areas in the pelage. We studied habitat selection of Antarctophthirus microchir on South American sea lion pups (Otaria flavescens Shaw, 1800) from Patagonia, Argentina, during the austral summer of 2009. We found a clear pattern of habitat selection: eggs are laid on the dorsal surface; nymphs 1 hatch there and then migrate to the belly, where they develop into adults and copulate; and then ovigerous females return to the dorsal surface. On the one hand, nymphs 1 are characterised by their low locomotory ability; therefore, the fact that they migrate as soon as they hatch suggests a clear pressure leading to microhabitat restriction. On the other hand, the described pattern of microhabitat selection seems to respond to the physiological requirements of each stage, which vary according to the physiological process considered, e.g. oviposition, morphogenesis, hatching and development. Accordingly, it appears that A. microchir would prefer the host's ventral area for development and copulation and the dorsal area for oviposition. However, the causes of this pattern are not clear, and many factors could be involved. Considering that sea lion pups periodically soak at high tides, and that prolonged immersion and very high humidity are known to be lethal for lice eggs, selecting the dorsal area would be advantageous for oviposition because it dries much faster. Furthermore, because humidity should be retained for longer periods on the ventral surface of the pup, wetter conditions on the sea lion would prevent desiccation of the nymphs in the very arid environment where O. flavescens breeds.