Low phosphorus (P) availability induces changes in root architectural traits thereby enabling the root to enhance P acquisition. We investigated the response of 89 diverse wheat genotypes to low (5 µM) and sufficient (500 µM) P in terms of root traits at seedling stage. Results revealed a large genetic variation in root traits under low P. Significant enhancement in total root length (TRL), surface area (TSA), volume (TRV), total root tips (TRT), total root forks (TRF) and crossings (TRC), root dry weight (RDW) and root-to-shoot ratio (RSR) were observed at low P as compared to sufficient P. Low P resulted in significant reduction in total P uptake and average root diameter. Analysis of genotype and genotype × trait showed that the principal components (PC) 1 and 2 governed 69.2 and 70.7% variability at sufficient P and low P, respectively. Among traits, average root diameter contributed 38.7% variability at sufficient P and 49.5% at low P. Under low P, significant correlations were observed between TRL and TSA (r = 0.94), TSA and TRV (r = 0.91), TRL and TRC (r = 0.90). The higher percentage distribution for root traits (TRL, RSA, RV and RT) was recorded in 0–0.5 mm diameter class under both P concentrations. Clustering of genotypes based on relative values revealed that in cluster III and IV, all root traits were enhanced in comparison to cluster I and II. Good performers in cluster III included BABAX, CARAZINHO, HD 2891, MARINGA and SUNCO. Genotypes grouped under cluster IV included BT-SCHOMBURGK, BWL 5200, KYPO 328 and OLYMPIC. Results of the current study could be used to develop P efficient genotypes with reduced dependency on P fertilizers.