The Na+/H+antiporter NhaC family protein is a kind of Na+/H+exchanger from the ion transporter (IT) superfamily, which has mainly been identified in the halophilic bacteria ofBacillus. However, little is known about the Na+/H+antiporter NhaC family of proteins in the extremely halophilic archaea. In this study, two Na+/H+antiporter genes,nhaC1andnhaC2, were screened from the genome ofNatronorubrum daqingensebased on the gene library and complementation of salt-sensitiveEscherichia coliKNabc. A clone vector pUC18 containingnhaC1ornhaC2could make KNabc tolerate 0.6 M/0.7 M NaCl or 30 mM/40 mM LiCl and a pH of up to 8.5/9.5, respectively. Functional analysis shows that the Na+(K+, Li+)/H+antiport activities of NhaC1 and NhaC2 are both pH-dependent in the range of pH 7.0–10.0, and the optimal pH is 9.5. Phylogenetic analysis shows that both NhaC1 and NhaC2 belong to the Na+/H+antiporter NhaC family of proteins and are significantly distant from the identified NhaC proteins fromBacillus. In summary, we have identified two Na+(K+, Li+)/H+antiporters fromN. daqingense.