The Rice Research and Development Institute (RRDI) of Sri Lanka has developed five exportable rice cultivars; At 362, Bg 94-1, Bg 360, Bg 1165-2, and Bw-Bs-1-2-31.The present study was conducted to establish the identities of these five cultivars at caryopsis level in comparison compared to those of mega rice cultivars (Bg 352, Bg 300, Bg 358, Bg 359, Bg 357, Bg 379-2, and At 353) in Sri Lanka using DNA fingerprinting and sequencing. These rice cultivars were grown in a greenhouse and a field using breeder-seeds. The seeds were harvested and subjected to a morphometric analysis using decision tree algorithms based on the size and colour of seeds and caryopses. The algorithms estimated the percentage accuracy of detection based on morphometric analysis ranged from 3.13-84.38 %. Similar seed and caryopsis combinations were grouped and exposed them to a panel of human subjects to discriminate the samples in each combination and subjected the data to calculate Kappa (K) and inter-rater reliability (IRR) statistics. The K was always 0.00, and IRR was 27% implying the inability of accurate visual differentiation. In the DNA fingerprinting analysis, a set of six SSR markers (RM206, RM246, RM251, RM335, RM475, and RM23744) were selected that can establish the cultivar identity. In addition, the combined analysis of DNA sequencing of 12 cultivars with three selected loci, (Seq 7-8, HvSSR12-34 and RM23744) authenticated the varietal identities.