The effects of waterlogging and salinity on seedling emergence, seedling growth and ion accumulation in a euhalophyte Suaeda salsa in an intertidal zone and on saline inland soil were investigated. Seedlings of S. salsa from the intertidal zone emerged more rapidly than those of the inland population under both waterlogged and drained conditions. Waterlogging and salinity had no adverse effects on seedling emergence of S. salsa from the intertidal zone, but markedly inhibited this parameter in the inland population. Waterlogging did not affect the seedling survival, shoot dry mass, and shoot height in high salinity in S. salsa from the intertidal zone, while the opposite trend was shown in the inland population. The root dry mass was higher in S. salsa from the intertidal zone as compared to the inland population, in waterlogged treatments by 1.9, 1.3, and 1.5 times in 1, 200, and 600 mM NaCl, respectively, and in drained treatments by 1.8, 2.3, and 3.0 times in 1, 200, and 600 mM NaCl, respectively. Waterlogging increased Na+ and K+ concentrations in high salinity, but waterlogging had no effect on Cl- concentration in shoots of S. salsa from the intertidal zone. In all NaCl treatments, waterlogging had no effect on concentrations of these ions in shoots of S. salsa from the saline inland site. In a field investigation, the fresh mass of shoots and roots were lower, whereas the root/shoot ratio was 1.5 times higher in S. salsa from the intertidal zone, compared with the inland population. These findings indicate that S. salsa population from the intertidal zone is more waterlogging tolerant than the inland population. S. salsa from the intertidal zone produced relatively more root biomass and this might help anchor plants against tidal action in the intertidal zone. The physiological and morphological characteristics may determine the natural distributions of the two S. salsa populations in their different saline environments.