<p>Identification of rice varieties with tolerance to Al³⁺ toxicity and P deficiency and their judicious utilization in breeding program could be one of the most economical and environment-friendly approaches towards increasing crop productivity in north-eastern regions predominated by acidic soil conditions. A set of 92 rice genotypes, including five released varieties as checks, was evaluated for yield and component traits in field conditions, as well as root and biomass traits in modified ammonium nitrate-free formulations of Yoshida and Magnavaca solutions for low P and high Al conditions, respectively. The Marker-trait association was also validated using north-eastern genotypes with a set of 13 gene-based Markers associated with high Al and low P. The genotypes under Al toxicity conditions had expressed stunted root length and an increased number of secondary roots. In the case of P-deficient conditions, roots were elongated and expanded with more secondary roots in search of P. The polymorphism information content for 13 gene-specific Markers associated with high Al and low P tolerance ranged from 2 to 4, with a mean of 2.31 per locus. Based on AMOVA, 90.85% of variation was observed due to differences among individuals within the population. Model-based clustering has differentiated the genotypes into three Major clusters with 72 pure and 20 admixtures. Based on model-based clustering, 72 out of 92 rice genotypes depicted more than 80% genetic purity to their respective ancestry. Under the validation study, the gene-specific markers, namely K-46–2, RM 258, and ART-1, were associated with tolerance in high Al and low P conditions as per the general linear model (GLM) and mixed linear model (MLM) study. Based on our studies, superior genotypes with higher performances in field and hydroponics, namely, Manipur Special, GR-12, Yemshea Ngha, Welhinyi Kezurd, and Chini Dhan, could be used in the development of acid-tolerant varieties vis-à-vis mapping of QTLs associated with low P and high Al tolerance.</p>