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The evaluation of the diversity in the cowpea local varieties (CLVs) allows the efficient use of genetic resources for cultivar development. This study aimed to evaluate the diversity of CLVs based on observation of morphological characteristics and to identify the relationship among morphological traits and potential varieties as donor genes to improve yield potential. The CLVs were collected from five provinces in Indonesia during 2017–2018. The evaluation of the performance of CLVs’ morphological characteristics was carried out in the Indonesian Legumes and Tuber Crops Research from March to July 2019. The observed data were 43 agronomic characters which consist of qualitative and quantitative characters. There is a high variation in stem pigmentation and seed color in 214 CLVs. There were nine qualitative characters with no variation. Most quantitative characters showed significant variation among CLVs. The clustering of 214 CLVs results in five clusters in which some CLVs maintain valuable characteristics that could be used in the breeding program. The number of pods per plant, number of racemes per plant, and 100 seed weight were useful for indirect selection in the yield improvement. Based on the genotype by trait biplot, the CLV 112, 191, and 111 could be used as donor parents for seed size improvement and the CLV 169 could be used as a donor parent for the yield potential improvement in the cowpea breeding program. Four cowpea genotypes can be recommended for commercial release or used as potential breeding material in cowpea cultivar development programs. The new findings of this study could provide a basis for the genetic improvement of cowpea.