Background Chenopodium quinoa Willd., a halophytic crop, shows great variability among different genotypes in response to salt. To investigate the salinity tolerance mechanisms, five contrasting quinoa cultivars belonging to highland ecotype were compared for their seed germination (under 0, 100 and 400 mM NaCl) and seedling's responses under five salinity levels (0, 100, 200, 300 and 400 mM NaCl). Results Substantial variations were found in plant size (biomass) and overall salinity tolerance (plant biomass in salt treatment as % of control) among the different quinoa cultivars. Plant salinity tolerance was negatively associated with plant size, especially at lower salinity levels (< 300 mM NaCl), but salt tolerance between seed germination and seedling growth was not closely correlated. Except for shoot/root ratio, all measured plant traits responded to salt in a genotype-specific way. Salt stress resulted in decreased plant height, leaf area, root length, and root/shoot ratio in each cultivar. With increasing salinity levels, leaf superoxide dismutase (SOD) activity and lipid peroxidation generally increased, but catalase (CAT) and peroxidase (POD) activities showed non-linear patterns. Organic solutes (soluble sugar, proline and protein) accumulated in leaves, whereas inorganic ion (Na+ and K+) increased but K+/Na+ decreased in both leaves and roots. Across different salinity levels and cultivars, without close relationships with antioxidant enzyme activities (SOD, POD, or CAT), salinity tolerance was significantly negatively correlated with organic solute and malondialdehyde contents in leaves and inorganic ion contents in leaves or roots (except for root K+ content), but positively correlated with K+/Na+ ratio in leaves or roots. Conclusion Our results indicate that leaf osmoregulation, K+ retention, Na+ exclusion, and ion homeostasis are the main physiological mechanisms conferring salinity tolerance of these cultivars, rather than the regulations of leaf antioxidative ability. As an index of salinity tolerance, K+/Na+ ratio in leaves or roots can be used for the selective breeding of highland quinoa cultivars.