This study examined the morphological traits of 63 cocoa varieties that have been imported and cultivated in Vietnam. These cocoa varieties were collected from five regions in Southern Vietnam and were classified into three groups based on their phylogenetic relationships. Their morphological features were individually evaluated and analysed. This included 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 has a bilobed anther with the exception of trilobed anther 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 various colours. Additionally, an anatomical analysis on the midrib structure of the leaves from the 63 varieties showed the highest similarity, likewise the stem structure. The colour of young leaves was observed as being green and red. This is the primary research that scrutinizes the morphological biodiversity of Vietnamese cocoa varieties during the three-decade development of the Vietnam cocoa project. The results have a practical applicationsfor cocoa cross-breeding and botanical taxonomy.