Vietnam has the appropriate climate, soil, and humidity for cocoa cultivation and is growing as a cocoaproducing country. To supply the international cocoa market, trees have been planted in Southern Vietnam. Cocoa quality depends on various factors, such as the genotype/cultivar, environment, and post-harvest processing. Until now, little research has been done on the genetic background  of vietnamesecocoa.Therefore,thisstudyfocusedonthegenetic relationships of 75 cocoa cultivars, sampled in Vietnam. Fourteenmicrosatellitemarkerswereusedtoassaythegenetic diversity and to genotype and differentiate the accessions. Descriptive statistics showed that most of the used microsatellite markers were sufficient to be used in further analysis, of which mTcCIR 15, 33, and 37 were the most polymorphic. The principal coordinate analysis (PCoA) and Bayesian clustering approach divided the samples in two groups, which were linked to the Trinitario and Forastero varieties. The Vietnamese Can Tho (CT) cultivars showed little variation, while the Thu Duc (TD) cultivars showed a continuous variation between the different reference cultivars. This indicates that the CTcultivars were Trinitario and that the TD cultivars were hybrids of Forastero or Forastero and Trinitario. The molecularcharacterizationisanimportantsteptowardsdeveloping a strong genetic basis for the Vietnamese cocoa industry.Itcanbeusedtoconservevaluablegeneticmaterialandto select promising cocoa cultivars which are disease resistant, high yielding, and fine flavored. In this way, the high-quality Vietnamese cocoa production can be improved and maintained.