Single nucleotide polymorphisms and restriction digestion-based haplotype variations among 160 flood prone rice varieties were analyzed with enzymes Alu I and Cac8 I to generate polymorphisms at Sub1A and Sub1C loci(conferring submergence tolerance), respectively. Haplotype associated with phenotype was used to study the haplotype variations at Sub1A and Sub1C loci and to determine their functional influence on submergence tolerance and stem elongation. Three patterns at Sub1A locus, Sub1A0(null allele), Sub1A1(does not cut) and Sub1A2(one SNP), and four patterns at Sub1C locus, Sub1C1, Sub1C2,Sub1C3 and Sub1C4, were generated. Both tolerant Sub1A1 and intolerant Sub1A2 had the same length, but the difference was presence of a restriction site in the Sub1A2, but absent at the Sub1A1. Further, two types of polymorphism were detected at the Sub1C, one included major length polymorphisms(165, 170 and 175 bp) and the other was a single restriction site at different position. Eight haplotypes(different combinations of the two loci), A1C1, A1C2, A1C4, A2C2, A2C4, A0C2, A0C3 and A0C4, were detected among 160 varieties. Haplotype A1C1 was comparatively more related to haplotypes A1C2 and A1C4, having the same Sub1A allele, and these haplotypes were found only in Bangladeshi, Sri Lankan and Indian varieties. Most tolerant varieties in A1C1 haplotype showed slow elongation, having tolerant specific Sub1A1 and Sub1C1 alleles. Further, the varieties Madabaru and Kottamali(A2C2) also showed moderate level of tolerance without Sub1A1 allele. These varieties were different with FR13 A and also suspected to carry different novel tolerant genes at other loci. These materials could be used for hybridization with Sub1varieties for pyramiding additional tolerant specific alleles into a single genotype for improving submergence tolerance in rice. Single nucleotide polymorphisms and restriction digestion-based haplotype variations among 160 flood prone rice varieties were analyzed to enzymes Alu I and Cac8 I to generate polymorphisms at Sub1A and Sub1C loci (conferring submergence tolerance), respectively. Haplotype associated with phenotype was used to study the haplotype variations at Sub1A and Sub1C loci and to determine their functional influence on submergence tolerance and stem elongation. Three patterns at Sub1A locus, Sub1A0 (null allele), Sub1A1 (does not cut) and Sub1A2 (one SNP), and four patterns at Sub1C Both tolerant Sub1A1 and intolerant Sub1A2 had the same length, but the difference was present from a restriction site in the Sub1A2, but absent at the Sub1A1. Further, two types of polymorphisms were detected at the Sub1C, one included major length polymorphisms (165, 170 and 175 bp) and the other was a single restriction site at different position. Eight haplotyp Haplotype A1C1 was comparatively more related to haplotypes A1C2 and A1C4, having the same Sub1A allele, and the same number of haplotypes A1C1, A1C2, A1C4, A2C2, A2C4, A0C2, A0C3 and A0C4, and these haplotypes were found only in Bangladeshi, Sri Lankan and Indian varieties. Most tolerant varieties in A1C1 haplotype showed slow elongation, having tolerant specific Sub1A1 and Sub1C1 alleles. Further, the varieties Madabaru and Kottamali (A2C2) also showed moderate level of tolerance without Sub1A1 allele. These varieties were different with FR13 A and also suspected to carry different novel tolerant genes at other loci. These materials could be used for hybridization with Sub1varieties for pyramiding additional tolerant specific alleles into a single genotype for improving submergence tolerance in rice.