This study was completed to enhance the morphology and anatomy data of twenty cocoa cultivars (Theobroma cacao L.) which widely grow in the Southern Vietnam. Reproductive organs and plant organs were analyzed and compared based on both the morphological characteristics and anatomical tissue. These cocoa clones analysis were selected from established procedures by various researchers. Two groups of hybrid were known for having Criollo characteristic and Forastero features. Further, the Forastero hybrid group could strongly be identified on samples: TD 5, TD 6, TD 7, TD 9, TD 11, TD 13, CT 5, CT 6 and CT 21. They have Amelonado pod set and yellow/orange yellow peel. Meanwhile, the Criollo hybrid could be described on samples: CT 7, CT 8, CT 9, TD 1, TD 2, TD 8, TD 12, TD 14,TD 3, TD 6, TD 10 (with Cundeamore/Angoleta pod set) and TD 3, TD 6, TD (with red/orange-red peel). The tissue anatomy and floral description were not differ among samples. This work showed significant results for further biomolecular researches and contributed in breeding programs, conservation and variety selection activities.