The present investigation evaluated 50 vegetable pigeonpea genotypes including five checks using alpha lattice design with three replications during kharif 2023-24 at college of agriculture, vijayapura with aim to assess the genetic diversity of vegetable pigeonpea genotypes using morphological and molecular markers to identify promising genotypes for breeding programs. Among the 50 genotypes, five were most promising genotypes viz., icpl 22503, icpl 22507, icpl 22497, icpl 22492 and icpl 22511 exhibited superior performance compared to the best check, early kamica, for green pod yield and its related traits. Genetic diversity was evaluated through mahalanobis d² and cluster analysis, revealed significant divergence among genotypes based on green pod yield and its related traits. Ward’s d² cluster analysis grouped 50 genotypes into five major clusters. The analysis of individual trait contributions indicated that the number of pods per plant, 100 seed weight, and days to 50 per cent flowering were the most significant factors influencing genetic differentiation.The estimates of genetic variability, heritability and gam were high for 100 green seed weight. Phenotypic correlation revealed a positively significant interrelationship between green seed yield and average green pod weight. The phenotypic path coefficient analysis was undertaken to ascertain the direct and indirect impact of various green pod yield, revealing that the average green pod weight exhibited the most pronounced direct effect on green pod yield.Molecular characterization using snp markers provided a reliable assessment of genetic diversity, with upgma clustering divided the genotypes into four main groups. The amova showed that 98.30 per cent of genetic variation was within samples, suggesting high adaptability and resilience. Structure analysis further identified four distinct genetic clusters, illustrating complex admixture patterns among the genotypes. Overall, the combined use of morphological and molecular markers offered comprehensive insights into the genetic diversity and structure of vegetable pigeonpea genotypes, emphasizing the importance of selecting genetically diverse genotypes to enhance breeding outcomes.