To begin marker assisted selection or marker assisted back cross breeding for introgression of a desirable trait into a variety from the donor genotype, study of parental polymorphism is a pre-requisite. Unless the parents are polymorphic for the traits of interest, the further selection of plants carrying the traits of interest is not possible in the progenies. The experiment was conducted in Directorate of Rice Research, Hyderabad. In the present study Rice microsatellite (RM) markers were used to study the parental polymorphism between the selected two parents APMS-6B a popularly used maintainer line with low stigma exsertion (14.95%) and BF-16B, another maintainer line with high stigma exsertion (80.25%). The two parents were screened for parental polymorphism using 454 SSR markers, of which 118 markers exhibited polymorphism. The overall polymorphism level for the surveyed SSR markers was 25.99 % across the 12 chromosomes. Construction of a Linkage Map could be ensued procuring the generated genotyping data which could further avail QTL analysis and identification of markers linked to stigma exsertion trait.