Discriminatory morpho-metric features are obvious on legume seeds. This study utilized seven quantitative and 11 qualitative seed traits to characterize 139 African yam bean (AYB) breeding lines which were developed through single seed descent procedure. The seven quantitative data were subjected to analysis of variance, their means were combined with qualitative scores for genetic distance, principal component (PC) and clustering analyses. Significant (P ≤ 0.001) variation existed among the breeding lines for the seven traits. Mean ranges of seed length (SL), width (SW), thickness (ST) and a single seed weight (SSW) among the 139 breeding lines were respectively: 6.77–10.22 mm, 5.70–7.86 mm, 4.96–7.45 mm and 0.15–0.42 g. Positive and significant (P ≤ 0.05) genotypic correlation existed among SSW, SL, SW and ST. Seed colours, pattern, shapes, sizes, surface texture, brilliance varied among the breeding lines. Ranges of phenotypic and genotypic coefficient of variation and broadsense heritability were: 5.49–23.84%, 2.95–19.88% and 28.91–69.54% respectively. Fourteen (quantitative and qualitative) traits contributed higher (≥ 0.30) eigenvector loadings to the first three PC axes which explained 57.9% of the total variation among the breeding lines. Similarity among the lines was 0.75. Four clusters ensued in the dendrograph and each group had genetic similarities of: 0.85 (I), 0.82 (II), 0.78 (III) and 0.80 (IV). This research unveiled significant variation among AYB breeding lines with promising reliability for breeding opportunities of the qualitative and quantitative seed traits, which could contribute to higher grain yield and acceptability.