The experiment comprising 35 genotypes of A. sativum including few commercial cultivars collected from different parts of the country and maintained in the Division of Vegetable Science, IARI, New Delhi was conducted to analyse diversity at morphological and molecular levels. The 11 yield related quantitative traits were studied and subjected to Mahalanobis D2 analysis. Among 60 primers screened, 21 were polymorphic and informative enough to analyse these genotypes. A total of 120 markers were generated with 97.69% of polymorphism. Each primer amplified between three and nine bands. Based on molecular analysis, pair-wise genetic distance (GD) ranged from 0.25 to 0.84, suggesting a wide genetic base for the genotypes. Based on morphological diversity, the genotypes were grouped into 8 clusters, while based on molecular analysis, they were clustered into 5 groups. Diversity based on morphological and molecular data was not in consonance with ecological distribution. The study showed that multivariate analysis method could be a useful way to discriminate the garlic genotypes.