English grain aphid (EGA) is a destructive insect pest of wheat. To identify the loci associated with EGA resistance and tolerance, 70 bread wheat accessions mainly from central Asia were evaluated for EGA resistance and tolerance traits at two locations, and genotyped with 51 SSR markers. Totally, three accessions showed high or moderate levels resistance and 17 genotypes displayed highly or moderately tolerate to EGA. Genetic diversity of these lines was investigated also. After 97 SSR loci which evenly covered all wheat chromosomes were scanned for association, four SSR loci were significantly associated with EGA resistance and four with EGA tolerance. After association analysis was conducted with dynamic aphid densities, we found four loci Xgwm192b, Xgwm391, Xbarc98, and Xgwm613b were detected continuously at different growing stages of wheat. In addition, the loci of EGA resistance/tolerance and Russian wheat aphid resistance were compared. The results generated in this study would be helpful for utilization of the EGA resistance/tolerance germplasm, and for development of mapping populations in EGA resistance breeding programs.