A salt-sensitive mutant designated rice salt sensitive 2 (rss2) was isolated from the M2 generation of the rice cultivar Nipponbare (Oryza sativa L. ssp. japonica) mutagenized with ethyl methanesulfonate (EMS). This mutant exhibited a greater decrease in salt tolerance with a significant increase in Na+ content in its shoots. Genetic analysis indicated that the increase in Na+ in rss2 was controlled by a single recessive gene. Further genome-wide analysis of the linkage map constructed from the F2 population of rss2/Zhaiyeqing 8 (ZYQ8) showed that two quantitative trait loci (QTLs) on chromosomes 1 and 6 were responsible for the Na+ concentration in shoots, which explained 14.5% and 53.3%, respectively, of the phenotypic variance. The locus on chromosome 1, but not that on chromosome 6, was also detected in the F2 population of Nipponbare/ZYQ8, suggesting that the QTL on chromosome 6 was responsible for the salt sensitivity in rss2. By analyzing the recombination events in 220 mutant individuals of an enlarged mapping population of rss2/ZYQ8, the rss2 locus was precisely mapped to an interval of 605.3 kb between insertion/deletion (InDel) markers IM21962 and IM22567. This finding will facilitate the cloning of the rss2 locus and provide insight into the physiological mechanisms of salt sensitivity in rice. This mutant highlighted rice salt sensitive 2 (rss2) was isolated from the M2 generation of the rice cultivar Nipponbare (Oryza sativa L. ssp. Japonica) mutagenized with ethyl methanesulfonate (EMS). This mutant exhibited a greater decrease in salt tolerance Genetic analysis indicated that the increase in Na + in rss2 was controlled by a single recessive gene. Further genome-wide analysis of the linkage map constructed from the F2 population of rss2 / Zhaiyeqing 8 (ZYQ8 ) showed that both quantitative trait loci (QTLs) on chromosomes 1 and 6 were responsible for the Na + concentration in shoots, which explained 14.5% and 53.3%, respectively, of the phenotypic variance. The locus on chromosome 1, but not that on chromosome 6, was also detected in the F2 population of Nipponbare / ZYQ8, suggesting that the QTL on chromosome 6 was responsible for the salt sensitivity in rss2. By analyzing the recombination events in 220 mutant i ndividuals of an enlarged mapping population of rss2 / ZYQ8, the rss2 locus was precisely mapped to an interval of 605.3 kb between insertion / deletion (InDel) markers IM21962 and IM22567. This finding will facilitate the cloning of the rss2 locus and provide insight into the physiological mechanisms of salt sensitivity in rice.