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This study describes the intraspecific variation of 30 edible-seed Lagenaria siceraria germplasm accessions from the University of Abobo-Adjame. These accessions were collected from three (Centre, East and South) geographical zones of Cote d'Ivoire. Selection based on seed size by the farmers has resulted in subdividing the species into two cultivars: large-seeded and small-seeded. The morphological diversity study of the collection included 18 accessions and 24 traits. The multivariate analysis of variance (MANOVA) showed a significant difference between the two groups of cultivars. Principal component analysis on 13 traits pointed out variations among individuals, mainly on the basis of flower, fruit, and seed size. Dendrogram with UPGMA method allowed clustering of the cultivars. The genetic structure analysis among accessions using allozyme markers showed the following values: 18.95% for the proportion of polymorphic loci (P), 1.21 for the number of alleles (A) and 0.053 for observed heterozygosity (Ho). The level of the within accessions genetic diversity (H-S = 0.188) was higher than the genetic variation among accessions (D-ST = 0.082). The estimates of F-statistics indicated a low level of genetic differentiation between accessions (F-ST = 0.298). Such a value suggested that L. siceraria maintains about 30% of its genetic variation among accessions. Nei genetic distances between the two cultivars were also low (0.002), indicating that cultivars were genetically similar enough to belong to the same genetic group.