There is no clear history of longan development in Indonesia even though it has developed well in Indonesia for many years. The study aimed at revealing genetic of diversity of local longan was done in Indonesian Citrus and Subtropical Research Institute (ICSFRI) from March to April 2008. ISSR markers were employed to identify the genetic variation among eight morphologically more or less alike accessions of longan ssp. Matrix data was counted and dendogram of samples was constructed using UPGMA and SAHN method. The cluster showed similarity value 0.34-0.86. The highest similarity value was observed between KL I and KL II (0.86) while the lowest one was obtained between KL I and KL V/KL VI (0.34). ISSR markers were able to identify the genetic diversity of longan and were helpful to provide information on genetic diversities especially for future breeding programs