Jackfruit (Artocarpus heterophyllus) is a large species in Moraceae family which is commonly found in Mekong delta of Vietnam. The demand of jackfruit products is presently increased for domestic consumption and processed export purposes. Nevertheless, breeding materials of jackfruit are insufficient since the identification of breeding material is mainly based on morphological characteristics. The effective applications of molecular markers to evaluate the genetic diversity of plants for enhancing the accuracy of plant breeding have been reported in different plants. In this study, two molecular markers namely RAPD and ISSR were applied to investigate the genetic variation of 20 jackfruit accessions collected in Mekong delta provinces in Southern Vietnam. The obtained results showed that both RAPD and ISSR markers produced a high number of polymorphic bands ranging from 8 to 12 and 3 to 8 bands, respectively. Based on the PIC values, the primers used by both markers are highly informative which are 0.69 or higher. The similarity coefficients are variable, ranged from 0.40-0.80 and from 0.41 to 0.81 for RAPD and ISSR, respectively. The phylogenetic analysis showed that collected jackfruit accessions were classed in different clusters with coefficient index varying from 0.52 to 0.87 suggesting the large variation in genetic composition of the jackfruit population in Vietnam. The findings could be potential to employ in future classification, conservation and development of this plant in the region.