Kalonunia is a traditional black-husked non-Basmati type scented rice of terai region (foothills of eastern Himalayas) of West Bengal, India. With a view to develop the morpho-genetic database of the unique variety, the field test was conducted at Bidhan Chandra Krishi Viswavidyalaya (BCKV), Kalyani, West Bengal, India during kharif (wet) season of 2013, 2014 and 2018, and molecular characterization was done at Bose Institute, Kolkata. The plants of Kalonunia were long-statured (scale 7, 145 ± 5 cm height), which had late heading (119 ± 4 days) and late maturity (scale 7, 151 ± 5 days). The bi-sexual flower had six yellow-coloured anthers and white-coloured feathery stigma. The black-husked matured grain was short in size (7.2 mm) with occasional mediumsized black awns (mean awn length 7.6 mm) and low test weight (15.2 g). The white-coloured kernels belonged to medium-slender group (length 5.12 mm and breadth 1.94 mm), which had low amylose content (18.1%), medium gelatinization temperature (alkali value 3.9) and medium-strong aroma (score 2.3). Among 23 simple sequence repeat (SSR) markers used for DNA amplification profile to develop molecular base-pair length database, only three (RM 182, RM 339 and RM 341) could make greater genetic distances (321.4 vs. 296.3 bp, 177.2 vs. 143.1 bp and 142.4 vs. 175.0 bp, respectively) between Kalonunia and international check IR 36.