The genetic diversity of thirty accessions of Bhut jolokia collected from three states of North-East India were studied for genetic diversity using Inter Simple Sequence Repeat (ISSR) marker. Genetic diversity analysis showed 54.5% of polymorphism with dissimilarity ranged from 0.08 to 0.43. Based on the banding pattern, the cluster analysis was done which distributed all the accessions in three distinct clusters. Present investigation revealed wide ranges of genetic variation and ISSR marker found to be useful tool for the diversity studies.