A subset of 275 F7 RIL population derived from a cross between indica cultivars Danteshwari and Dagad Deshi were used to identify the QTLs associated with root and shoot architecture. The phenotypic evaluation was done for eight root traits and four shoot architecture related traits. The RIL population was genotyped using 93 SSR and 11 SNP markers distributed over the entire twelve rice chromosomes. QTL mapping using single marker analysis leads to the identification of 24 markers putatively associated to 10 traits. The total number of markers associated was 1 for root length, 1 for root dry weight, 1 for root/shoot length ratio, 1 for root/shoot dry weight ratio, 3 for root volume, 3 for shoot fresh weight, 3 for tiller number, 6 for shoot dry weight, 8 for shoot length and 11 for total plant length. No markers were associated with root fresh weight and root/shoot fresh weight ratio. Four markers HvSSR01-80, HvSSR01-86, HvSSR01-87 and HvSSR04-26 were found to be strongly associated with total plant height and shoot length. HvSSR05-12 was found to be strongly associated with shoot fresh weight and shoot dry weight. The negative additive effect and LOD > 2.4 of these marker-traits indicating the majority of the favorable alleles for traits are contributed by the landrace, Dagad Deshi which has deep/long roots. The QTLs identified for root and shoot traits will be helpful for the rice molecular breeding programs.