Root development at the seedling stage is an important trait for the early growth of rice. In this study, the root length and weight of 211 Korean landrace rice at the seedling stage were evaluated, and the average root length and weight were 6.94 cm and 48.18 mg, respectively. Principal component analysis (PCA) of 211 accessions based on 70,849 SNPs presented three subgroups. Two quantitative trait loci (QTLs) associated with root length were detected on chromosomes 3 and 6 using genome-wide association study (GWAS). Four haplotypes were identified using associated SNPs for the two root length QTLs. The average root length of Hap2 and Hap 3 was 7.32 cm and 6.56 cm, respectively, and were significantly different. Gene expression analysis in the candidate regions of QTLs for root length at the seedling stage showed that several genes were expressed in the root. QTLs associated with root length at the seedling stage identified in this study may be applied to improve the root length trait and detect candidate genes.