Phosphorus (P) is an essential nutrient for rice growth. The scarcity of rock phosphate, the main source of P fertilizer, has prompted breeders to seek rice genotypes tolerant to P deficiency by exploring Pup1 locus, which plays a role in the P uptake, among the rice genotypes. This study was aimed at exploring Pup1 locus among 55 rice genotypes to identify genotypes possesing Kasalath alleles at four specific markers of genes in the Pup1 locus and high similarity of nucleotide sequence of the markers compared to Pup1 locus reference sequence. Amplification of genomic DNA of three check genotypes, i.e. Kasalath, NIL-C443, and Nipponbare; 36 upland, 15 lowland, and 1 amphibian rice, with K05&#8722;1, K20&#8722;2 + Bsp12861, K29&#8722;1, and K46&#8722;2 markers, showed that the number of upland rice containing Pup1 locus was comparable to lowland rice (49% and 47.3%, respectively). Three genotypes, i.e. Gajah Mungkur, Cabacu, and IR36, contained Kasalath alleles on the four markers, indicating that they have Pup1 locus. Kasalath, NIL-C443, Gajah Mungkur, Cabacu, and IR36 had varying levels of nucleotide sequence similarity based on K20&#8722;2 + Bsp12681 and K46&#8722;2 marker regions, ranged from 54.7&#8722;95.2% and 94.6&#8722;97.5%, respectively, compared to the Pup1 reference sequence. Based on Kasalath allelic pattterns and high nucleotide sequence similarity to the Pup1 reference sequence (87.3&#8722;92.4% and 94.6&#8722;96%, respectively), Gajah Mungkur, Cabacu, and IR35 were identified as new sources of Pup1 locus to replace Kasalath.