The limited availability of Phosphorus (P) in the soil poses a significant challenge to of rice productivity in rainfed tropical regions. There has been a constant demand of diverse donors for enhancing tolerance to P‐deficient soils. In this study, we evaluated 181 aus rice accessions of the 3000 Rice Genome Project (3 K‐RGP) for grain yield and six other agronomical traits under control (~20 mg kg−1 available P) and low‐P (8–10 mg kg−1 available P) field trials. The objectives were to assess the level of low‐P tolerance in the aus germplasm and select stable high‐yielding accessions using stress tolerance attributes. We also surveyed the presence of PSTOL1 gene and Pup1 polymorphisms to find the effect of PSTOL1 as well as t Pup1 haplotypes on low‐P tolerance. Principal component analysis (PCA) using five stress tolerance attributes revealed that attributes like mean productivity (MP) and stress tolerance index (STI) are useful for selecting high‐yielding accessions with stable yield under stress and control conditions. Notably, accessions like Kalabokari, Devarasi, ARC 12021, Jasure Aus, ARC 7336 and ARC 12101 had higher level of tolerance than the check varieties Vandana and Sahbhagi Dhan. Majority of aus accessions carried the PSTOL1 gene (73%) and had the tolerant haplotype of Pup1 (65%) like the tolerant checks. Although, at large, the PSTOL1‐positive accessions were more vigorous, and high yielding under low‐P, there were a few PSTOL1‐negative aus accessions showing higher level of tolerance. The findings suggest that non‐PSTOL1 type tolerance exists in aus rice which needs to be substantiated through further studies.