Root System Architecture (RSA) and shoot morpho-developmental traits are crucial for the adaptation of crops to diverse environments and farming settings. In this study we report the characterization of a 183 accessions élite durum wheat association panel for RSA and shoot morphological traits. Plants were grown in controlled conditions up to the 7th leaf (late tillering) using the high-throughput phenotyping platform GROWSCREEN-Rhizo, a rhizo-box-based system consisting of 90 cm deep rhizo-boxes integrated with automatic root RGB imaging. The experimental set-up permitted the dynamical assessment of the length of the three main root classes (seminal, later and nodal), the distribution of each root class in the rhizo-box profile, maximum root system depth and width. Leaf area and both leaf and tiller number were measured twice per week whereas chlorophyll content was estimated by SPAD twice during the experiment. Root and shoot dry biomass were collected at the end of the experiment. The dynamic collection of the above-mentioned traits allowed us to model root and shoot growth and thus to disentangle the final point phenotypes in simpler phenes. A genome-wide association study (GWAS) based upon the Illumina Infinium 90K SNP revealed 180 QTLs controlling RSA and/or shoot growth traits (P < 0.0001). Root and shoot QTLs were mostly independent each other as well as QTLs for different root classes traits. For nodal root traits only most of the QTLs (6/9) overlapped with shoot QTLs. Among others, three chromosomal regions on chromosome 1BS, 6AL and 7AS exhibited a marked influence in root and shoot morphoarchitectural traits. Indeed, in a relatively short portion (7.5 cM) of chromosome 1BS we observed significant segregation for 10 root and shoot traits, with concordant allelic effect direction. A 6 traits QTL cluster on chromosome 6AL confirmed the role of this region in the control of root gravitropism observed in Maccaferri et al., 2016. A QTL cluster on chromosome 7AS was found to be significantly associated with root length and depth, root specific weight and shoot/root dry biomass ratio. Haplotypes segregation at this QTL cluster revealed a contrasting selection pattern between sub-populations of the panel. Indeed, the most root-oriented haplotypes clearly prevailed in lines selected in the Mediterranean basin (Italy and ICARDA) while shoot-oriented haplotypes are predominant in lines selected by CIMMYT in well-watered breeding set-up. These results suggest an indirect but major role of RSA and root/shoot equilibrium in durum wheat breeding and environmental adaptation.