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A study was undertaken to evaluate the simple sequence length polymorphism in six aerobic rice genotypes in order to elucidate their genetic differentiation at molecular level using six microsatellite primer pairs. Additionally, the primer pairs were validated using twelve inter-genotypic mixtures for their utilization in genetic purity assessment of these aerobic rice genotypes. Statistical methods and parameters used for deriving inference were polymorphism percent, polymorphism information content, discrimination and non-discrimination coefficient, similarity coefficient and analysis of divergence. Polymorphism was recognized among the genotypes on the basis of presence or absence of bands, besides variation in number and position of bands. Considering the number of alleles generated in conjunction with the level of polymorphism detected and discrimination ability exhibited, the primers RM 263, RM 5359 and RM 337 appeared to be highly polymorphic and comparatively more informative for the purpose of genetic differentiation of entries under evaluation. Molecular profiling data based on these three primer pairs allowed easily recognizable differentiation of the inter-genotypic mixtures from referral genotypes at least with a single marker allele difference. The complementary banding patterns visualized in inter-genotypic mixtures served as discrete molecular tags for distinguishing the referral genotypes and inter-genotypic mixtures. These three microsatellite primers may be further utilized in genetic purity assessment and authentication of aerobic rice genotypes.