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Using a suite of morphological traits and neutral molecular markers, we have reevaluated the origins of the two cultivated jute species. The nine Corchorusspecies, which are restricted to both Africa and Asia, were phenotyped for bast fibre yield- and quality-linked traits, morpho-phenetically classified based on those traits’ similarities, genotyped by nuclear microsatellites and haplotyped by chloroplast microsatellites. The two cultivated jute species contain ~70% of the neutral genetic diversity present in their wild relatives. Phylogenetic analyses using 38 highly polymorphic nuclear microsatellites identified C. aestuansas the common ancestor to both the cultivated jute species. C. urticifoliusis the nuclear progenitor of C. olitorius(dark jute), but no close nuclear progenitor of C. capsularis(white jute) could be identified. Although either C. aestuansor C. pseudo-olitoriusor both appear to be the possible cytoplasmic progenitors of white jute, the matrilineal ancestry of dark jute remains obscure. However, the presence of a single, unique chloroplast haplotype in each of the two cultivated species indicates the involvement of other unknown wild relatives. Taken together with archaeobotanical evidence, our results suggest that dark jute had its origin in equatorial region of east Africa, but was domesticated in India. We could not support an Indo-Myanmar origin of white jute, and possibly it also originated in Africa, but was domesticated in Asia.Using a suite of morphological traits and neutral molecular markers, we have reevaluated the origins of the two cultivated jute species. The nine Corchorusspecies, which are restricted to both Africa and Asia, were phenotyped for bast fibre yield- and quality-linked traits, morpho-phenetically classified based on those traits’ similarities, genotyped by nuclear microsatellites and haplotyped by chloroplast microsatellites. The two cultivated jute species contain ~70% of the neutral genetic diversity present in their wild relatives. Phylogenetic analyses using 38 highly polymorphic nuclear microsatellites identified C. aestuansas the common ancestor to both the cultivated jute species. C. urticifoliusis the nuclear progenitor of C. olitorius(dark jute), but no close nuclear progenitor of C. capsularis(white jute) could be identified. Although either C. aestuansor C. pseudo-olitoriusor both appear to be the possible cytoplasmic progenitors of white jute, the matrilineal ancestry of dark jute remains obscure. However, the presence of a single, unique chloroplast haplotype in each of the two cultivated species indicates the involvement of other unknown wild relatives. Taken together with archaeobotanical evidence, our results suggest that dark jute had its origin in equatorial region of east Africa, but was domesticated in India. We could not support an Indo-Myanmar origin of white jute, and possibly it also originated in Africa, but was domesticated in Asia.