Populus euphratica Oliv. is of high salinity tolerance and used as a model species for investigating molecular mechanisms of trees’ responses to salt stress. In the work presented here the researchers found that calli of P. euphratica grew more rapidly and accumulated less Na+, but more K+, under salt stress than those of salt-sensitive poplar, Populus hopeiensis. Different types of Na+/H+ antiporters (SOS1, NhaD1 and NHX1) were isolated from P. euphratica; all of these genes have been shown to play important roles in plant salt tolerance mechanism in previous studies. Expression profiles of these three genes were compared between P. hopeiensis and P. euphratica in the presence and absence of salt stress by real-time PCR. The three genes were induced in both P. euphratica and P. hopeiensis by salt. Transcript levels of PeNHX1 were lower in P. euphratica than in P. hopeiensis under 150 mM NaCl stress. In addition, transcript levels of PeNhaD1 were lower, while PeSOS1 were higher in P. euphratica than in P. hopeiensis under both stressed and unstressed conditions. The results indicated that P. euphratica up-regulates different genes and consistently maintains both effluxes of Na+ and high K+ levels. Our data suggests that differences in gene expression patterns may contribute to the difference in salt tolerance between these two poplars.