The present invention relates to a three way sampling method for assessing Genetic Purity (GP) of seed lot and crop plants at DNA fingerprinting laboratory. The method facilitates in carrying out seed based analysis for MAT and leaf based analysis for MAP. The method comprises the steps of collecting and sorting seeds and leaf samples, wherein the selected seeds and leaf samples are sliced into three parts, two parts are arranged in matrix and used for respective row and column bulking while third part is used for individual assessment for identifying potential contaminant in the seed lot and crop plant. The method provides a rapid and time saving technique for speedier testing of genetic purity of seed lots and crop plants.