Sorghum (Sorghum bicolour (L.) Moench) grown under rain-fed conditions is usually affected by drought stress at different stages, resulting in reduced yield. Determining the genetic control of root system architecture (RSA) in plants via multi-locus genome-wide association study (GWAS) is very important to improve moisture stress resistance in sorghum. The objective of this study was, therefore, to identify genomic regions underlying RSA traits in sorghum at the early growth stage among 200 genotypes. A total of 124 QTNs were identified on all chromosomes that are significantly linked with the nine root and shoot traits using one or more of the six ML-GWAS models, with a LOD score threshold of ≥ 3. Among these identified QTNs, a total of 38 significant QTNs were identified in at least two ML-GWAS models. Out of the 38 detected QTNs, 28 were co-located with previously reported QTLs for the RSA, while the remaining 10 QTNs were distinct. We identified 438 co-localized genes within a 65 kb window upstream and downstream of 38 QTNs for studied traits. Among these genes, 153 were uncharacterized or unknown while the rest of the genes have protein description. Moreover, 16 genes contained the QTNs intergenic region of within the gene's sequences. These genes may regulate root development in the seedling stage. Further analysis on these genes might be important to explore the genetic structure of RSA of sorghum.