In order to understand the genetic basis of salt tolerance in wheat， the SNP loci and candidate genes which were significantly associated with salt tolerance were explored. Three hundreds of wheat varieties （ lines） were subjected for tests of salt tolerance using 200 mmol/L NaCl and normal nutrient solution， respectively， and these varieties were genotyped with 90 K chips exploring 16650 polymorphic SNPs. The statistical analysis was performed by using the Q+K association mixing model for eight root traits including the longest root length， root dry weight， root fresh weight， average root diameter， root tip number， root surface area， root volume and total root length. The results showed that the root traits showed extensive phenotypic variation， with a coefficient of variation of 24.3% to 50.0%， and a polymorphic information content（ PIC） of 0.170-0.562， as well as a genome-wide LD attenuation distance of 6 Mb. Three subgroups were suggested by population structure analysis， including： Subgroup I， which included 143 genotypes（ 47.67%） mainly from Henan， Shaanxi， and Sichuan provinces； Subgroup II， which included 74 genotypes（ 24.67%） mainly from Beijing； Subgroup III， which is represented by 83 lines（ 27.67%） mainly from Henan. Seventy-seven SNP loci（ P ≤ 0.001） were detected by genome-wide association study to be significantly associated with salt tolerance traits， and they were distributed on 20 chromosomes except chromosome 6D in wheat. Each of SNPs contributed to 3.70% to 19.45% of phenotypic variation， in which 6 loci such as RAC875_c13169_459 on chromosomes 1A， 3A， 4A， 7A， 3D， and 5D are simultaneously associated with two or more traits， with a contribution rate of 3.78%-19.45%. Based on the physical positions of 77 SNP loci， 17 candidate genes associating with wheat salt tolerance have been proposed. For example， TraesCS5B01G031800（ Cation/H （ +） antiporter） might play an important role in the transport of cations such as Na+； TraesCS5A01G329000 （ Defensin） might play a role in blocking the entry of cations such as Na+. TraesCS2A01G079000（ Repetitive proline-rich cell wall protein） might function in the formation of cell walls. Collectively， these candidate genes which have been identified from this study are proposed as important genes for salt tolerance in wheat.