Bixa orellana L., is a natural food dye yielding plant belonging to the family Bixaceae. It yields a non-toxic, edible Food dye Bixin and Nor-Bixin also popularly known as Annatto having orange-red colour and has a huge demand in the dairy industry to colour food products. In the present study, the 2 accessions of Bixa orellana L with white and rose-coloured flowers both bearing green capsules with green spines in common were identified from west and south of Bangalore city (Bangalore

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... and Lalbagh), Karnataka, India. These 2 accessions were analyzed for intraspecific variations with respect to the morphology, Genetic relatedness and Dye (Bixin) content. Our studies report that these 2 accessions were highly diverse and exhibited maximum variations with respect to habit and other morphological parameters. Hence these 2 accessions were subjected to SSR (Single Sequence Repeat) Marker studies. The analysis of SSR data showed high level of genetic variations. Out of 10 SSR primers, 7 primers showed polymorphism between the two accessions. A total of 43 discernible and reproducible SSR bands were generated by employing 7 selected primers. Out of them, 22 bands were polymorphic. The number of bands produced per primer ranged from 1-8. The markers described in this study could be of use in marker assisted selection, genetic improvement and breeding programmes and could help in the utilization and germplasm conservation of Rosecoloured flower and Green capsuled with green spined accession of Bixa orellana L., in systematic scientific breeding programmes which also yields maximum bixin content. Index Terms: Bixa orellana L., Bixin, green capsule, green spines, rose colour flower, SSR markers and white colour flower.