The upland rice ecology is usually low in available phosphorus. A major QTL Pup1 related to P-uptake is very much important for upland rice. In the present study, ninety six genotypes mainly upland cultivars and landraces were genotyped for better P-uptake. Forty six numbers of genotypes possessed the Pup1 locus that accounts for 47.92% of the total genotypes considered. Seventy six genotypes (79.17%) showed probable presence of PSTOL1 gene. The cluster analysis could group the upland, aerobic and irrigated genotypes into different subgroups. The genotypes N22, Dinoroda, Bowde, Bamawpyan, Tepiboro, Karni, Lalsankari, Surjamukhi, Hazaridhan, and Kalinga III were positive for two closest flanking and two gene specific Pup1 markers and formed distinct cluster. The genotypes possessing the Pup1 QTL can be taken as donor lines to be used in marker-assisted breeding programmes for incorporation of the QTL into high yielding popular varieties to increase their phosphorus uptake efficiency.