Plant biotechnologist frequently have to analyze the genotype of multiple polymorphic loci. For multi-sample or multilocus genotyping, many researchers employ labor-intensive methods, such as cleaved amplified polymorphic sequences, restriction fragment length polymorphisms and simple sequence repeats (SSR). To develop races for a particular constraint of plant production, genotypes are very beneficial to plant breeders and application of modern tools like DNA markers such as SSR to these genotypes will help for further insight into rice genome and to develop rice with more resistance to the biotic and abiotic constraints of modern ecosystem. Hence the present investigation on molecular characterization of genotypes will strengthen the germplasm units for their better usage which in turn would affect the yielding ability of plant. The importance of having a large set of SSR markers is to provide a bridge for moving rapidly and efficiently from phenotype to sequence information and vice-versa, and providing a foundation for understanding the evolutionary consequences of sequence variation.