Availability of markers that distinguish commercially important premium Basmati rice varieties from cheaper Basmati or non-Basmati indica rice varieties is of interest to exporters, commercial suppliers and consumers to ensure the varietal purity of Basmati rice supplies. In this study, a fingerprint database of 27 rice varieties including commercially important traditional Basmati (TB), cross-bred (evolved) Basmati and some non-Basmati indica rice varieties has been prepared using 50 microsatellite markers. A total of 271 electromorphs (alleles) were detected at 50 SSR (simple sequence repeat) loci, 92 of which were observed only in 2–10 of the 16 Basmati rice varieties. Notably, 7–10 of the sixteen Basmati rice varieties had the same Basmati specific electromorphs at RM562, RM551 and RM547 loci. Alarge number of unique (22) and null (16) electromorphs were noticed in Basmati rice varieties. A combination of four SSR markers (RM224, RM248, RM547 and RM594) can be used to differentiate all the 27 rice varieties. Specific SSR markers have been identified for the authentication of Premium Basmati rice cultivars such as Taraori Basmati (RM547, RM594 and RM511), Basmati 370 (RM252, RM426 and RM527), Karnal Local (RM248, RM423 and RM488) and Pusa 1121 (RM252, RM400 and RM410), and for the detection of adulterant like Sharbati (RM215, RM423 and RM259). SSR database reported here, shall broaden the list of SSR markers already recommended for varietal identification and detection of adulteration in Basmati rice supplies.