This study was carried out to analyze the polymorphic region of exon 1 of OsHKT1;5 of 22 high yielding rice varieties that are salt tolerant. The result of the phenotypic screening for salinity stress was done using the standard protocol of the International Rice Research Institute which recorded that all rice varieties developed very well under control condition, 85.38% were quite tolerant to salinity treatment of 4‰, 68.18% were moderately tolerant to salinity treatment of 8‰ and 36.36% were moderately tolerant to salinity treatment of 10‰, similar to Pokalli. The result of sequencing exon 1 region of OsHKT1;5 gene recorded five Single Nucleotide Polymorphisms (SNP) markers. Five nucleotide substitutions in coding sequence of OsHKT1;5 were found at the positions: 382, 418, 484, 551 and 994. All five non-synonymous nucleotide substitutions caused changes in amino acids (D51N, P63A, V86I, R107H and H255D).