Sixty genotypes with different seed coat colour and seed sizes were evaluated for seed longevity under both natural and accelerated ageing over seasons. The genotypes were grown during rabi, 2018, and summer, 2021, and freshly harvested seeds were used. For natural ageing, seeds were stored in a cloth bag in ambient condition and were removed at bimonthly intervals till 20 months. Accelerated ageing was carried out as per International Seed Testing Association (ISTA) guidelines. The germination percentage after natural and accelerated ageing over two seasons was determined. The correlation between two seasons of accelerated ageing and month-wise natural ageing was highly significant. The principal component analysis (PCA) using seed longevity grouped the majority of black genotypes into a separate cluster. Higher seed longevity was associated with black seed coat colour and small seed size. Microsatellite marker-based clustering also produced a separate cluster for majority of black genotypes and grouped the genotypes into a large number of clusters suggesting high diversity in the plant material. Two black seed coat colour genotypes, ACC No.369 and ACC No.39 consistently showed higher longevity under natural and both the years of accelerated ageing and serve as a source of alleles for higher seed longevity in soybean.