Two Khao Dawk Mali 105 (KDML105) chromosome segment substitution lines (CSSLs) that carry quantitative trait loci (QTL) for drought tolerance (DT) on chromosome 8 (CSSL KDML105 DT-QTL8) were used in this study (designated CSSL-94 and CSSL-116). This CSSL population was developed from a cross between KDML105 (drought and salt sensitive) and DH103 (drought tolerant). Physiological responses in roots to short-term salt stress during early seedling growth were investigated in CSSL-94, CSSL-116, KDML105 and DH103. Seven-day-old seedlings were treated with 150 mM NaCl for 3 days. Measurements of root growth, Na+/K+ ratio, proline (Pro) content, malondialdehde (MDA) and ascorbate peroxidase (APX) activity as well as gene expression levels particularly that of aquaporins (AQPs; genes controlling water uptake) revealed that CSSL-94 was the most salt-tolerant. The ability to maintain ion homeostasis and the highest level of AQPs expression are presumed to be important mechanisms which conferred salt tolerance to this line.