This study aimed to clone and sequence Na (+) / K (+)-ATPase (nka) α-subunit isoforms from, and to determine their mRNA expression levels and protein abundance in the brain of the African lungfish, Protopterus annectens during the induction, maintenance and arousal phases of aestivation in air. We obtained the full cDNA sequences of nkaα1, nkaα2 and nkaα3 from the brain of P. annectens. Phylogenetic analysis of their deduced amino acid sequences revealed that they are closer to the corresponding NKA α-subunits of tetrapods than to those of fishes. The mRNA expression of these three nkaα isoforms showed differential changes in the brain of P. annectens during the three phases of aestivation. After 12 days of aestivation, there was a significant increase in the protein abundance of Nkaα1 in the brain of P. annectens. This could be an important response to maintain cellular Na(+) and K(+) concentrations and regulate cell volume during the early maintenance phase of aestivation. On the other hand, the mRNA expression of nkaα2 decreased significantly in the brain of P. annectens after 6 months of aestivation, which could be a result of a suppression of transcriptional activities to reduce energy expenditure. The down-regulation of mRNA expression of nkaα1, nkaα2 and nkaα3 and the overall protein abundance of Nka α-subunit isoforms in the brain of P. annectens after 1 day of arousal from 6 months of aestivation were novel observations, and it could be an adaptive response to restore blood pressure and/or to prevent brain oedema.