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Most of Khyber Pakhtun Khwa (KPK) rice growing regions face problems of rapid floods each year which results soil erosion. Our current study aims to conserve the local varieties of rice growing in these floods alarming regions. About 40 genotypes were collected and evaluated through SDS-PAGE for genetic diversity. Sodium Dodicyle Sulphate Polyacrylamide Gel Electrophoresis protocol for seed storage protein profile of 40 genotypes were resolved adjusting the conditions on 12.25-15%. The experimental results from banding profile of 40 genotypes were evaluated statistically for cluster analysis and genetic disagreement. For more accuracy the electrophorogram of gels replicate were divided into three zones. The results from cluster analysis and genetic disagreement showed that present investigation was useful as provided information about 100% genetic relationships of genotypes, and with average low similarity coefficient and genetic variation of genotypes. These variations are due to the differences among various ecological conditions. However further collection and advance techniques are requires broadening the gene pool.