Serendipita indicais an endophytic root symbiont fungus that enhances the growth of various plants under different stress conditions, including salinity. Here, the functional characterization of two fungal Na+/H+antiporters, SiNHA1 and SiNHX1 has been carried out to study their putative role in saline tolerance. Although their gene expression does not respond specifically to saline conditions, they could contribute, together with the previously characterized Na+efflux systems SiENA1 and SiENA5, to relieve Na+from theS. indicacytosol under this stressed condition. In parallel, anin-silicostudy has been carried out to define its complete transportome. To further investigate the repertoire of transporters expressed in free-living cells ofS. indicaand during plant infection under saline conditions, a comprehensive RNA-seq approach was taken. Interestingly,SiENA5was the only gene significantly induced under free-living conditions in response to moderate salinity at all the tested time points, revealing that it is one of the main salt-responsive genes ofS. indica. In addition, the symbiosis withArabidopsis thalianaalso inducedSiENA5gene expression, but significant changes were only detected after long periods of infection, indicating that the association with the plant somehow buffers and protects the fungus against the external stress. Moreover, the significant and strongest induction of the homologous geneSiENA1occurred during symbiosis, regardless the exposure to salinity. The obtained results suggest a novel and relevant role of these two proteins during the establishment and maintenance of fungus-plant interaction.