To identify quantitative trait loci controlling salinity tolerance in cucumber, a total of 432 simple sequence repeat (SSR) markers were screened on two cucumber inbred parental lines, 11411S (salt tolerant) and 11439S (salt sensitive). Genotypic analysis was conducted using F2 individuals while F2:3 population was used for phenotypic evaluation and quantitative trait loci (QTL) analysis. Sixty polymorphic markers obtained from the parental screening were tested on the F2 individuals along with parental lines. Six markers (SSR20710, SSR13312, SSR1667, SSR23627, SSR13021 and SSR 00398) with unambiguous banding patterns were subjected to simple regression analysis to determine the significant marker-trait association. Salinity tolerance was evaluated by visual scoring (TOL), the survival rate (SU) and relative leaf numbers (RLN14). The SU, TOL, and RLN14 were higher in the tolerant parent than sensitive one. The mean scores of F2:3 families exhibited continuous variation and some had values outside the parental means. SSR20710 located on chromosome 3 explained 16.5%, 7.1%, 5.6% and 7.8% of variations observed in SU, TOL, RLN14 and percent green leaves (%GL), respectively. Markers SSR13312 and SSR16667 contributed 25% and 59% of RLN14 and TOL, respectively. This study provided valuable information for future genetic studies of salinity tolerance in cucumber and marker assisted selection for salinity tolerance improvement in cucumber.