Njavara is a medicinal rice strain, endemic to Kerala, South India, bestowed with medicinal qualities. Genetic variations and some of the physicochemical properties were studied using standard molecular protocols and compared with those of nonmedicinal rice varieties: Jyothi and IR 64. Njavara showed 11 unique positive and 36 unique negative markers to differentiate it from Jyothi and IR 64. Genetic similarity coefficient studies showed two well-defined clusters separating Njavara from Jyothi and IR 64. All the three varieties had waxy gene Wxa allele. Njavara had (CT)n repeats at (CT)10, while Jyothi and IR 64 had repeats at (CT)11 in the 50-untranslated region of waxy gene. Njavara showed a CGTG sequence, while Jyothi and IR 64 had a CGCG sequence at the 14th exon of Sbe 1 gene. Njavara, Jyothi, and IR 64 have similar amylose equivalent (AE), which was confirmed by microsatellite markers. The SSR primers for protein content and setback viscosity primer (RM 4608) were observed to be polymorphic in case of Njavara. Njavara rice, with a distinct gene pool and medicinal properties, can be exploited as a nutraceutical rice.