In this study, metagenomic DNA was screened for the Na+/H+ antiporter gene from the halophilic bacteria from Daban Salt Lake using Escherichia coli KNabc lacking three major Na+/H+ antiporters, and two genes psmrAB predicted to encode paired small multidrug resistance (PSMR) family proteins, the homolog of YvdSR, were finally cloned. Only the simultaneous presence of psmrAB, but not the single gene alone, conferred the tolerance of E. coli KNabc to up to 0.6 M NaCl and at alkaline pH. pH-dependent Na+(Li+)/H+ antiport activity was detected from everted membrane vesicles prepared from E. coli KNabc cells carrying psmrAB, which had the highest activity at pH 9.0. However, a detailed test for antimicrobial drugs showed that E. coli DH5α with psmrAB only exhibited slight resistance to chloramphenicol, but not other representative antimicrobial drugs especially ethidium bromide. Protein sequence alignment showed that neither PsmrA nor PsmrB has homology with known single-gene or multiple-gene Na+/H+ antiporters, or such proteins as TetA(L) and MdfA with Na+/H+ antiport activity. Taken together, PsmrAB should function mainly as a novel two-component Na+/H+ antiporter. This is the first example of a PSMR family member that exhibits Na+/H+ antiporter activity.