The experimental material comprising ten tomato genotypes collected from Vegetable Research Station, Junagadh Agricultural University, Junagadh. Eight morphological characters used, namely plant height, number of branches, plant spread, fruit length, fruit girth, seed per fruit, shape of fruit and color of fruit for morphological characterization. Three isoenzymes viz Esterase, Peroxidase, Catalase and protein profile of seedlings used for Biochemical characterization. 11 RAPD, 13 ISSR, 23 SSR primers were used for molecular characterization. In present study, the morphological variation present at morphological level in ten tomato genotypes was studied using the eight characters, analysis of variance also showed significant variation in six quantitative characters among all ten tomato genotypes, genotype GT-1 showed the maximum plant height (80 cm) and plant spread (45.6 cm), while genotype JTL-04-49 showed maximum fruit length (8.85 cm) and fruit girth (19.6 cm) and genotype JTL-08-33 and JTL-08-14 showed highest No. of branches and seeds per fruit respectively. There were no variation in qualitative characters namely shape of fruit and color of fruit among ten tomato genotypes