【Objective】 Root improvement is one of the key factors to improve stress resistance and yield of wheat. Root architecture related genes, homoeologous TaDRO, are cloned from cultivars with different root phenotypes. Molecular markers are developed to detect its relationship with important agronomic traits of wheat. which could provide technical support for wheat improvement. 【Method】 Polymorphic sites of TaDRO-A, -B and -D were detected in 21 common wheat accessions with high diversity. Physical locations of three homoeologues were determined based on the newest genome sequence of Chinese Spring. Molecular markers were developed according to the polymorphic sites at TaDRO-5A and -5B. Association analysis between genotypes and phenotypic traits were carried out in a natural population of 323 accessions. 【Result】 The three homoeologous genes of TaDRO-A, -B and -D were cloned. TaDRO-A, -B and -D were located on chromosomes 5A (426.15 Mb), 5B (381.00 Mb) and 5D (327.60 Mb), respectively. Three SNPs were detected at TaDRO-A among 21 accessions and two haplotypes were formed, Hap-5A-A and Hap-5A-C. A molecular marker, TaDRO-5A-KASP, was developed based on the SNP located at position of -2271 bp in the promoter region. Thirteen SNPs and one InDel in the promoter region, four SNPs in the coding region were detected at TaDRO-5B, formed two haplotypes, Hap-5B-Ⅰ and Hap-5B-Ⅱ. The marker TaDRO-5B-InDel was developed based on the Indel at position of -300 bp. Association analysis showed that haplotypes of TaDRO-5A were significantly correlated with plant height (PH), thousand kernel weight (TKW) and root growth angle (RGA). The genetic effects on Hap-5A-A showed RGA and TKW increasing, and root depth and PH decreasing, while those on Hap-5A-C exhibited the opposite effect. The effects of Hap-5B-Ⅰ exhibited root depth and PH increasing, and TKW decreasing, while those of Hap-5B-Ⅱ were the opposite. Hap-5A-C and Hap-5B-Ⅰ were favored haplotypes in landraces while they were non-favored ones in modern cultivars. The frequencies of Hap-5A-C and Hap-5B-Ⅰ in arid and semi-arid areas were higher than those in wet areas in China. Hap-5A-C was favored haplotype in dry regions worldwide. Frequencies of Hap-5A-A and Hap-5B-Ⅱ were increasing in breeding process, respectively.【Conclusion】 Hap-5A-C and Hap-5B-Ⅰ are associated with deeper root, higher PH and lower TKW, whereas Hap-5A-A and Hap-5B-Ⅱ behave the opposite. Wheat cultivars showed root depth and plant height decreasing in breeding process due to development of irrigation system and nitrogen industries. The developed molecular markers might be used to select the ideotypes of cultivars for higher efficiency use of water and nitrogen.