The swamp eel, Monopterus albus, can survive in high concentrations of ammonia (>75 mmol l(-1)) and accumulate ammonia to high concentrations in its brain (4.5 µmol g(-1)). Na(+)/K(+)-ATPase (Nka) is an essential transporter in brain cells, and since NH4(+) can substitute for K(+) to activate Nka, we hypothesized that the brain of M. albus expressed multiple forms of Nka α-subunits, some of which might have high K(+) specificity. Thus, this study aimed to clone and sequence the nka α-subunits from the brain of M. albus, and to determine the effects of ammonia exposure on their mRNA expression and overall protein abundance. The effectiveness of NH4(+) to activate brain Nka from M. albus and Mus musculus was also examined by comparing their Na(+)/K(+)-ATPase and Na(+)/NH4(+)-ATPase activities over a range of K(+)/NH4(+) concentrations. The full length cDNA coding sequences of three nkaα (nkaα1, nkaα3a and nkaα3b) were identified in the brain of M. albus, but nkaα2 expression was undetectable. Exposure to 50 mmol l(-1) NH4Cl for 1 day or 6 days resulted in significant decreases in the mRNA expression of nkaα1, nkaα3a and nkaα3b. The overall Nka protein abundance also decreased significantly after 6 days of ammonia exposure. For M. albus, brain Na(+)/NH4(+)-ATPase activities were significantly lower than the Na(+)/K(+)-ATPase activities assayed at various NH4(+)/K(+) concentrations. Furthermore, the effectiveness of NH4(+) to activate Nka from the brain of M. albus was significantly lower than that from the brain of M. musculus, which is ammonia-sensitive. Hence, the (1) lack of nkaα2 expression, (2) high K(+) specificity of K(+) binding sites of Nkaα1, Nkaα3a and Nkaα3b, and (3) down-regulation of mRNA expression of all three nkaα isoforms and the overall Nka protein abundance in response to ammonia exposure might be some of the contributing factors to the high brain ammonia tolerance in M. albus.