Abstract: Njavara the traditional rice cultivar used in Ayurvedic health care system in India is confined to the state of Kerala, India. The efforts for collection, conservation and documentation of this unique type are meager. Hence, the present study aimed in collection of Njavara types from different parts of the state and was subjected to morphological evaluation, isozyme and RAPD analysis for the characterization of ecotypes of this cultivar and identification of markers for distinguishing Njavara ecotypes from other rice cultivars. Among the qualitative characters apiculus colour, lemma and palea colour and seed coat colour showed great variability and hence, can be considered as markers for the identification of Njavara types. The isozyme analysis with alcohol dehydrogenase revealed two unique bands for Njavara ecotypes. A set of eleven RAPD markers were used for DNA profiling of the Njavara ecotypes and the DNA amplification exhibited unique bands with primers OPE 6, OPP 6 and 11. The pooled data for Jaccard ’s similarity coefficient values revealed that at similarity coefficients 0.33 and 0.41, based on isozyme and RAPD analysis, respectively. The genotypes were grouped into two clusters, one large cluster with Njavara ecotypes and one small cluster with two check varieties. The study revealed no duplicates among the Njavara accessions and also identified unique bands that can be used as markers for identification of the cutivar from other rice varieties.