This study was conducted to identify ISSR markers associated with RKN resistance trait in kenaf. Variety Gregg and Everglade 41 were used as resistant and susceptible parents in this study. All the parents as well as the F2 population developed from the cross of resistant and susceptible were inoculated with the RKN in the green house and their gall score was estimated after 42 days. Sixty ISSR primers were used to genotype parental and F2 population DNAs and results were analysed with electrophoresis system. We found thirteen (13) polymorphic ISSR markers between the resistant and susceptible parents. These 13 polymorphic markers were used to individually genotype 10 highly resistant and 10 highly susceptible F2 individual plants. Five ISSR markers appeared to be linked with RKN resistance. These five potential polymorphic markers were used to screen 102 individual F2 plants. Marker data showed that ISSR 801, ISSR 844, and ISSR 831 were significantly associated with the RKN gall index. Results also showed that 33.88 percent of the gall index variation was explained by ISSR 831, 33.72% by ISSR 801 and 33.71% by ISSR 844.
