Forty two fine grain rice varieties released from ANGRAU were studied in order to determine the molecular identity of Samba Mahsuri by using Genomic and EST SSR markers. Forty SSR primers amplified a total of 96 alleles with an average of 2.4 alleles per marker, RM 11278 was able to distinguish BPT 5204 from the remaining popular varieties by amplifying an allele of 270 bp. This primer was considered as a molecular ID for BPT 5204. Cluster analysis based on Jaccard's similarity coefficient using UPGMA grouped the 42 rice varieties into seven clusters. The clustering pattern was observed to be mainly based on the grain type and genetic background of the varieties. To utilize these SSR markers specific for Samba Mahsuri effectively for detection of impurities in Samba Mahsuri, a rapid and cost effective two-dimensional bulked DNA sampling strategy was designed and validated. The SSR marker RM 11278 was found to be an efficient tool in the process of quality control of BPT 5204.