Njavara (shashtika in Sanskrit), a rice (Oryza sativa L.) landrace described in ancient Sanskrit treatises of Ayurveda for its nutritive and medicinal properties, is traditionally used in Kerala for Ayurveda treatments. We characterized the genetic resources of Njavara using 24 morphological traits and 664 amplified fragment length polymorphic (AFLP) markers. Different multivariate methods revealed four morphologically distinct types (morphotypes) in the Njavara germplasm, which were Electronic supplementary material The online version of this article (