The presence of epidermal bladder cells (EBCs) in halophytes allows considerable amount of Na⁺ being accumulated in these external structures, away from the metabolically active mesophile cells. Also, stomatal patterning may represent a primary mechanism by which plants can optimise its water-use efficiency under saline condition. This investigation was aimed to explore the varietal differences in a salinity tolerance of quinoa (Chenopodium quinoa) by evaluating a broad range of accessions and linking the overall salinity tolerance with changes in stomatal characteristics and EBC parameters. One hundred and fourteen accessions were grown under temperature-controlled glasshouse under non-saline and 400 mM NaCl conditions, and different physiological and anatomical characteristics were measured. Accessions were classified into three classes (sensitive, intermediate and tolerant) based on a relative dry weight defined as salinity tolerance index (STI). Results showed a large variability in STI indicating a strong genetic variation in salinity tolerance in quinoa. Bladders density was increased in a majority of accessions under saline condition while the bladder’s diameter remained unchanged; this resulted in a large variability in a bladder’s volume as a dependant variable. Stomata density remained unchanged between saline and non-saline conditions while the stomata length declined between 3% to 43% amongst accessions. Leaf Na⁺ concentration varied from 669 μmol/gDW to 3155 μmol/gDW under saline condition and, with an exception of a few accessions, leaf K⁺ concentration increased under saline conditions. Correlation analysis indicated a significant positive association between EBC diameter and STI on one hand and EBC volume and STI on the other hand, in a salt-tolerant group. These observations are consistent with the role of EBCs in sequestration of toxic Na⁺ in the external structures, away from the cytosol. A negative association was found between EBC density and diameter in salt-sensitive plants. A negative association between STI and stomata length was also found in a salt-tolerant group, suggesting that these plants were able to efficiently regulate stomatal patterning to balance water loss and CO₂ assimilation under saline conditions. Both salt-sensitive and salt-tolerant groups had the same Na⁺ concentration in the shoot under saline conditions; however, a negative association between leaf Na⁺ concentration and STI in salt-sensitive plants indicated a more efficient Na⁺ sequestration process into the EBCs in salt-tolerant plants.