The purpose of this research was to explore the methodologies for extracting DNA from cocoa-derived products including cocoa leaves, cocoa beans, cocoa powder, cocoa butter, cocoa mass, and dark chocolate. For the DNA extraction CTAB-SDS (sodium dodecyl sulfate), DNeasy Plant kit and DNeasy Plant kit with polyvinyl polypyrrolidone (PVPP) have been used. The yield and purity of the DNA preparations were determined through spectrophotometry and analyzed by PCR. The results showed that the DNeasy Plant kit and the CTAB-SDS methods seemed appropriate for DNA purification from cocoa leaves, cocoa powder and cocoa mass. The CTAB-SDS procedure is mostly effective for DNA extraction from cocoa beans and dark chocolate. However, in all three examined procedures, the lowest DNA yield was obtained from the cocoa butter matrix. Apparently, the CTAB based method (CTAB-SDS) was the best for DNA extraction from almost all cocoa-derived products, except the cocoa butter. The 2nd focused on clarifying the genetic diversity of fourteen cocoa clones in Vietnam. Primers plant c and plant d were used to analyze the genetic relationship. All detected band were encoded into binary matrix and the dendrogram was generated using the program NTSYS-PC 2.1 The similarity matrix was subjected to cluster analysis by unweighted pair group method for arithmetic mean (UPGMA). The genetic clustering of 14 Cocoa varieties showed genetic differences ranged from 0 to 41%. At around 59% similarity, fourteen TD clones could be divided into three groups: A, B, and C. Group A had ten clones (TD1, TD2, TD3, TD5, TD6, TD7, TD8, TD9, TD11, TD12), in group B there were 2 clones (TD10 and TD13), and two clones belonged to group C (TD14 và TD15). Regarding homologous relationship within members of a group, B adopted 80%, while A and C had approximately 76.4% and 73% respectively. This result contributed important signification for Vietnamese Cocoa breeding and selection cultivar activities.