Eighty inter simple sequence repeat (ISSR) primers were applied to detect polymorphisms among eight durian clones. From eighty ISSR primers used, only six primers UBC824, UBC860, UBC886, UBC888,UBC889 and UBC891 generated distinct polymorphic fragments. Out of the total of 42 bands produced from six primers, eight were polymorphic. Only 5 fragments successfully cloned to convert into sequence characterized am-plified regions (SCAR) markers. Based on the sequences of the cloned ISSR fragments, six ISSR-SCAR primer sets were produced.Three SCAR markers designed from this study were examined using genomic DNA extracted from 4 accessions of Durio lowianusand Durio kutejensis and 6 accessions of hybrids and clones of Durio zibethinus.Resis-tance to Phytophthorainfection is an important objective for cultivar improvement programmes of Durian. Molecu-lar markers linked to such key traits can be used to screen resistant individuals for future breeding.ISSR-SCAR marker 886-2 was identified to separate the resistant and susceptible Durio speciestowards Phytophthorainfections.