V-H+-ATPase and Na+/K+-ATPase were localized in the gills and branchiostegites of M. amazonicum and the effects of salinity on the branchial chamber ultrastructure and on the localization of transporters were investigated. Gills present septal and pillar cells. In freshwater (FW), the apical surface of pillar cells is amplified by extensive evaginations associated with mitochondria. V-H+-ATPase immunofluorescence was localized in the membranes of the apical evaginations and in clustered subapical areas of pillar cells, suggesting labeling of intracellular vesicle membranes. Na+/K+-ATPase labeling was restricted to the septal cells. No difference in immunostaining was recorded for both proteins according to salinity (FW vs. 25 PSU). In the branchiostegite, both V-H+-ATPase and Na+/K+-ATPase immunofluorescence were localized in the same cells of the internal epithelium. Immunogold revealed that V-H+-ATPase was localized in apical evaginations and in electron-dense areas throughout the inner epithelium, while Na+/K+-ATPase occurred densely along the basal infoldings of the cytoplasmic membrane. Our results suggest that morphologically different cell types within the gill lamellae may also be functionally specialized. We propose that, in FW, pillar cells expressing V-H+-ATPase absorb ions (Cl-, Na+) that are transported either directly to the hemolymph space or through a junctional complex to the septal cells, which may be responsible for active Na+ delivery to the hemolymph through Na+/K+-ATPase. This suggests a functional link between septal and pillar cells in osmoregulation. When shrimps are transferred to FW, gill and branchiostegite epithelia undergo ultrastructural changes, most probably resulting from their involvement in osmoregulatory processes.