Bird’s eye chilli (Capsicum frutescens L.) is one of the most important species of the genus Capsicum, and is grown and consumed widely across north-east India, particularly in the states of Mizoram and Manipur. The bioactive compounds present in this landrace of north-east India are very less studied. The antioxidant property was assayed by scavenging abilities using diphenyl-2-picrylhydrazyl (DPPH), azinobisethylbenzothiazoline-6-sulphonic acid (ABTS), assay of ferric reducing antioxidant power (FRAP), and determining total phenolics (TP) and total flavonoids (TF) contents. There was a significant variation in the total phenolic content (12.4–133.2 mg GAE/g dry weight), total flavonoid (22.1–58.8 mg quercetin/g dry weight), DPPH (0.5–6.1 mM AAE/g dry weight), ABTS (20.5–44.3 mM AAE/g dry weight) and FRAP (0.7–7.8 mM GAE/dry weight) antioxidant capacity in Capsicum frutescens L. landraces. Two landraces of Capsicum chinense viz. MN-1 and MN-2 exhibited highest values for all the antioxidant assays. Positively significant correlation coefficients were observed between ABTS–FRAP, TF–FRAP, TP–FRAP, TP–DPPH and TP–TF. From principal component analysis (PCA) first two PCs explained 67.3 % of total variance and it was contributed mainly by TP, TF, ABTS and FRAP activities. Seventy-two Capsicum landraces were grouped into five clusters based on the standardized squared Euclidean distance using Ward’s hierarchical clustering method and separation based on PCA biplot. The experiment established that the landraces of Capsicum frutescens L. are potent source of natural antioxidants which reduce the oxidation processes in the body by protecting against reactive oxygen species.