Association analysis of yield-related traits and simple sequence repeat (SSR) loci distributed randomly in the peanut genome could contribute to marker-assisted selection breeding by the detection of elite alleles and the interaction of the gene region associated with high yield traits. We performed genome-wide association analysis with the mixed linear model (Q+K) by scanning 166 peanut germplasm with selected 64 SSR markers. In all, 166 peanut germplasm could be assigned to 7 subpopulations by population structure and cluster analysis, with results from both methods similar. The morphological characteristics and geographic origin of germplasm were consistent within model-based clusters. From 2011 to 2013, the number of detected SSR markers significantly associated with 6 yield-related traits was 20, 33 and 26 respectively; 13 markers (P<0.05) were detected repeatedly over 2 years. The mean rate of phenotypic explanation of SSR loci associated with traits was 0.067 3 (range 0.011-0.348 1). In total, 590 alleles were detected, with a mean of 12.29 alleles per SSR loci. Among all the trait-related markers, TC1A02 (P<0.001) had the highest rate of phenotypic explanation and contained 21 alleles, which was associated with the trait of pod number per plant. Among the SSR loci associated with the main effective factors of yield, the elite alleles with a high positive effect that could be used in marker-assisted selection of yield improvement were TC1A02-C560 (+40.926 1), TC1A02-C470 (+41.588 5), pPGPseq2E6-B473 (+63.953 4) associated with 100-pod weight, TC1A02-C500 (+7.374 4) associated with pod number per plant and GM1843-E157 (+4.316 6) associated with full pod number per plant.