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Phosphorous (P) fixation in soils with high free ferric oxides and aluminum in the clay fraction is a widespread problem and limits access of plants to P even if it is present in the soil. Problem is acute in upland situation. Therefore, a set of 31 rice genotypes comprising of adopted upland and lowland lines as well as aromatic and semi-dwarf high yielding cultivars were grown both in P-deficient as well as P-sufficient soil. P-uptake ability of these genotypes was compared when they were grown in P-sufficient as well as in P-deficient soil. Six genotypes (Gitanjali, Gobindabhog, Jaladhi, Pusa Saugandh, Radhunipagol, Tulaipanji) accumulated significantly more P per plant under both Psufficient (p less than 0.01) and P-deficient (p less than 0.01) conditions. Rice genotypes were also characterized by PCR-based markers, Pup-1 K42 and Pup-1 K29 which were linked with a major QTL for phosphate uptake-1 (Pup-1) locus. Haplotyping of Pup-1-K42 markers showed 918 bp amplification in nine genotypes but among them, only three genotypes showed higher P-uptake and dry-matter-weight in P-limiting condition. Unlike japonica germplasm, both K42 and K29 were not diagnostics in assessing Pup-1 locus in indica germplasm. Three Bengal landraces, Bhutmuri, Gobindabhog and Radhunipagol can serve as ideal donor parent for introgression of Pup1 locus. The markers validated in this study will help in the marker assisted introgression of P-deficiency tolerance in rice.