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Chilli, also known as hot pepper is an important vegetable and spice crop having immense commercial and export value. The present study was an attempt to select an elite cultivar of Chilli based on their varietal performance, structural, microscopic characterization and elemental analysis. In varietal performance analysis, Kashi Anmol with yield 725.05 g/plant, total soluble solid 6.74o Brix and ascorbic acid 132.53 mg/100 g was found superior to all other cultivars. No major difference was observed in the backbone structures of the green chilli powder of all the cultivars during X-Ray Diffraction analysis. Scanning Electron Microscopy revealed spherical and amorphous in form of the powder. EDAX traces elements like Carbon (58.45-72.63%), Oxygen (26.25-39.47%), Chlorine (0.15-0.27%), Potassium (0.49-1.64%) in all the cultivars except Magnesium (0.26 & 0.22%) and Aluminum (0.15 and 0.22%) which was observed in only two cultivars. The EDAX study also confirmed the absence of any health hazardous elements in the varietal sample. The presented study suggests the cultivation of Kashi Anmol as an elite Chilli variety in the study area as compared to others.