Estimation of genetic diversity along with phenotypic variation among crop germplasm is important for collection, conservation, evaluation and utilization in crop improvement programs. In the present study, 185 diverse genotypes of tomato (Solanum lycopersicon Mill.) including 33 genotypes of Lycopersicon var. Cersiforme were evaluated at morphological, biochemical and molecular level. Considerable variations were observed for quantitative and qualitative traits at morphological level during two consecutive years in 2016 and 2017. The minerals were estimated for potassium, magnesium, calcium, iron and zinc contents. However the antioxidant compounds including lycopene content, ascorbic acid, total soluble solids and beta-carotene. Cluster analysis revealed grouping of genotypes based on similarities indices irrespective of geographical origin. Correlation of yield with various agronomic traits displayed complex pattern of association. The germplasm depicted enough variation, 20 genotypes were identified based on agronomic performance. Studied toamto germplasm were also analyzed for molecular level using forty SRR markers to detect polymorphism. In conclusion 25 traits studied in a set of 185 genotypes described high range of variability for yield (kg), single fruit weight (g), plant height and potassium contents. Principal component analysis (PCA) with 40 SSRs markers revealed the sub-population structure of 185 accessions spread over two dimensions. Genetic diversity analysis, agronomic evaluation along with association of SSR markers with QTLs reported in the present study would be a bench-mark for breeders in targeting future tomato improvement for yield, quality, anti-oxidants and micro- minerals either through direct selection or through hybridization for developing pure lines or hybrids.