Longan (Dimocarpus longan L.) is an important fruit plant in Vietnam and therefore the demand of genetic conservation and variety authentication is of high importance. Due to the limitations of chemical and morphological longan characterization approaches, it is necessary to develop more precise DNA-based methods. In this study, we focused on developing SCAR (Sequence Characterized Amplified Region) markers for longan identification. The total of 11 longan accessions collected from different provinces in Vietnam were genetically characterized by using 20 RAPD (Random Amplified Polymorphic DNA) primers to identify polymorphic RAPD fragments. Twenty two polymorphic RAPD fragments were obtained and 2 of them were further sequenced and developed into SCAR markers. The sequences of specific RAPD fragments were used to design primers. Totally, 2 pairs of SCAR primers were archived. These primers showed significant effectiveness for cultivar identification of 2 favourite longan cultivars of Vietnam namely “Duong phen Hung Yen” and “Chin muon Hung Yen”.