Bhut Jolokia (Capsicum assamicum), one of the hottest chilli in the world is a chilli cultivar, endemic to North East India and is extensively cultivated in the states of Assam, Nagaland and Manipur. The demand of this chilli is very high in domestic as well as in the international market due to its extreme hotness and pleasant aroma. This plant is severely affected by leaf curl disease caused by Begomovirus, leading to total crop loss. Accurate diagnosis of this viral disease at seedling stage, prior to transplanting, is essential to prevent further spread of the disease. With an aim to device a rapid and accurate detection assay, Rolling Circle Amplification (RCA)-Polymerase Chain Reaction (PCR) technique was used for detection of the viral pathogen. RCA technique was employed to increase the viral template and PCR was conducted using a degenerate primer pair. With the help of this assay, 1.4 kbp segment of DNA-A genome of the Begomovirus was amplified. Phylogeny revealed close proximity of the isolate with Tomato leaf curl Bangladesh virus. This is the first report on characterization of Begomovirus infecting Bhut Jolokia in Tezpur region of Assam.