Aluminium toxicity is adversely affecting the rice growth and production in acidic soils of developing countries. Rice is popular and stable crop which meets food requirements of about 50% world population. A set of 122 rice backcross recombinant inbreed lines (BRILs) derived from a cross between Japonica (cv.02428) and Indica (Changhui/891) was grown in nutrient solution. High density linkage map generated by using 3075 highly stable SNP markers. Relative root length (RRL) was used as standard criteria for aluminium tolerance. A total of 23 QTLs were detected in the current study for six traits across all experimental conditions. Regarding RRL, three QTLs qCRL-6, qSRL-6, and qRRL-6 were found stable and common QTLs across all environments. Out of these three QTLs, qRRL-6 with higher heritability estimates (H² = 96.59%) was novel QTL with a positive additive effect. In addition, shoot length (SL), shoot fresh weight (SFW), root fresh weight (RFW), shoot dry weight (SDW) and root dry weight (RDW) were used and identified QTLs, qSSL-11, qRRFW-1, and qRRDW-1 and qRRDW-8 which were newly reported QTLs. Three pleiotropic QTLs qRRFW-1, qRSDW-1, and qRRDW-1 were also reported and these QTLs would facilitate to improve Al tolerance by MAS selection and QTLs pyramiding.