Bicarbonate (HCO ) transport mechanisms play an essential role in the acid-base homeostasis of aquatic animals, and anion exchange protein 3 (AE3) is a membrane transport protein that exchanges Cl/HCO across the cell membrane to regulate the intracellular pH. In this study, the full-length cDNA of () was obtained from the Pacific white shrimp (). The cDNA is 4,943 bp in length, contains an open reading frame of 2,850 bp, coding for a protein of 949 amino acids with 12 transmembrane domains. -AE3 shows high sequence homology with other AE3 at the protein level. mRNA was ubiquitously detected in all tissues selected, with the highest expression level in the gill, followed by the ovary, eyestalk and brain. By hybridization, positive cells were shown predominant localization in the secondary gill filaments. The expression levels of were further investigated during the essential life processes of shrimp, including ontogeny, molting, and ovarian development. In this case, the spatiotemporal expression profiles of in were highly correlated with the activities of water and ion absorption; for example, increased mRNA levels were present after hatching, during embryonic development, after ecdysis during the molt cycle, and in the stage IV ovary during gonadal development. After low/high pH and low/high salinity challenges, the transcript levels of were reduced in the gill, while the cell apoptosis rate increased. In addition, knockdown of mRNA expression induced cell apoptosis in the gill, indicating a potential link between -AE3 and gill damage. Altogether, this study thoroughly investigated the relationship between the mRNA expression profiles of and multiple developmental and physiological processes in , and it may benefit the protection of crustaceans from fluctuated aquatic environments.