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Gboma eggplant (Solanum macrocarpon L.) and jute mallow (Corchorus olitorius L.) are important indigenous vegetables of Africa. Even though these two indigenous vegetables are important in terms of nutrition, medicine and resilience of livelihoods, they have been neglected by scientific research and their value chain has not been developed. To ensure effective management and utilization of these important genetic resources in breeding programmes, it is important to collect their core collections. Therefore, eighteen different accessions of gboma eggplant and one hundred and six accessions of jute mallow were evaluated using RCBD with three replications. Results revealed diversity and significant variation among the various agronomic traits of both jute mallow and gboma eggplant. Correlation analyses between morphological traits of both species revealed positive and negative relationships, indicating predictable success for eventual breeding activities. Principal component analyses revealed traits of agronomic importance such as plant height, leaf length and number of leaves per plant as the most important traits for the distinction and separation of Corchorus olitorius accessions. The leaf blade length, leaf blade width, fruit colour at ripeness, plant height and fruit length were the most important traits for the distinction and separation of Corchorus olitorius accessions. Furthermore, hierarchical cluster analysis grouped the accessions into distinct clusters and accessions from the same geographical origin were classified separately. Nineteen accessions and six accessions were selected to constitute core collections of one hundred and six and eighteen accessions of jute mallow and gboma eggplant, respectively. Examination of the phenotypic traits showed that the genetic variation expressed for each trait in the entire collection has been preserved in the core collection. Core collections of these indigenous vegetables have many potential uses for the development of improved cultivars and should increase the utilization of germplasms of these important indigenous vegetables of Africa.