Synechococcus elongatus strain PCC 7942 is an alkaliphilic cyanobacterium that tolerates a relatively high salt concentration as a freshwater microorganism. Its genome sequence revealed seven genes, nha1 to nha7 (syn_pcc79420811, syn_pcc79421264, syn_pcc7942359, syn_pcc79420546, syn_pcc79420307, syn_pcc79422394, and syn_pcc79422186), and the deduced amino acid sequences encoded by these genes are similar to those of Na ؉ /H ؉ antiporters. The present work focused on molecular and functional characterization of these nha genes encoding Na ؉ /H ؉ antiporters. Our results show that of the nha genes expressed in Escherichia coli, only nha3 complemented the deficient Na ؉ /H ؉ antiporter activity of the Na ؉ -sensitive TO114 recipient strain. Moreover, two of the cyanobacterial strains with separate disruptions in the nha genes (⌬nha1, ⌬nha2, ⌬nha3, ⌬nha4, ⌬nha5, and ⌬nha7) had a phenotype different from that of the wild type. In particular, ⌬nhA3 cells showed a high-salt-and alkaline-pH-sensitive phenotype, while ⌬nha2 cells showed low salt and alkaline pH sensitivity. Finally, the transcriptional profile of the nha1 to nha7 genes, monitored using the real-time PCR technique, revealed that the nha6 gene is upregulated and the nha1 gene is downregulated under certain environmental conditions.