Na+/H+ exchangers (NHEs) regulate intracellular pH and ionic balance by mediating H+ efflux in exchange for Na+ uptake in a 1:1 stoichiometry. This study aimed to obtain from the ctenidium of the giant clam Tridacna squamosa (TS) the complete cDNA sequence of a NHE3-like transporter (TSNHE3), and to determine the effect of light exposure on its mRNA expression level and protein abundance therein. The coding sequence of TSNHE3 comprised 2886 bp, encoding 961 amino acids with an estimated molecular mass of 105.7 kDa. Immunofluorescence microscopy revealed that TSNHE3 was localized to the apical membrane of epithelial cells of the ctenidial filaments and the tertiary water channels. Particularly, the apical immunofluorescence of the ctenidial filaments was consistently stronger in the ctenidium of clams exposed to 12 h of light than those of the control kept in darkness. Indeed, light induced significant increases in the transcript level and protein abundance of TSNHE3/TSNHE3 in the ctenidium, indicating that the transcription and translation of TSNHE3/TSNHE3 were light-dependent. As light-enhanced calcification generates H+, the increased expression of TSNHE3/TSNHE3 in the ctenidium could be a response to augment H+ excretion in pursuance of whole-body acid-base balance during light exposure. These results signify that shell formation in giant clams requires the collaboration between the ctenidium, which is a respiratory and iono-regulatory organ, and the inner mantle, which is directly involved in the calcification process, and provide new insights into the mechanisms of light-enhanced calcification in giant clams.,© 2017 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of The Physiological Society and the American Physiological Society.