This study examined the morphological traits of sixty-three (63) cocoa varieties that have been imported and cultivated in Vietnam. These cocoa varieties were collected from five regions in Southern Vietnam. The morphological features were individually evaluated and analyzed, including the leaf characteristics (leaf and stem anatomy) and flower features (ligule shape, anther number, pollen, stamen and ovule, fruit, seed). The results of this study showed a large variation across all morphological characteristics of the evaluated cocoa varieties. The Vietnamese cocoa flower showed a diversity of morphological characteristics including five shapes of ligule (oval, broad, deltoid, elliptic, and sub-lanceolate) and each stamen also had dithecous anthers with the exception of tri-thecous anthers for TD11. Furthermore, the shape of pollen grains was found homogeneous in all 63 varieties. The colour of the stamens and ovules was purple and white respectively for all examined samples. Three kinds of fruit shapes were identified, namely Angoleta, Amelonado and Cundeamor, and these were of varied colours. The Vietnamese cocoa cultivars were classified into three groups based on their fruit morphology characteristics (Trinitario-Criollo, Trinitario-Forastero, and Trinitario). Additionally, an anatomical analysis on the midrib structure of the leaves from 63 varieties showed high similarities, likewise the stem structure. The colour of young leaves was observed as being green and red. This primary research scrutinizes the morphological biodiversity of Vietnamese cocoa varieties during the three-decade development of the Vietnam cocoa project. The results provide practical applications for cocoa cross breeding and botanical taxonomy.