Cultivated tomato (Solanum lycopersicum L.) an important vegetable crop is reported to have very low genetic diversity. The present study was conducted to determine the extent of heritable variation in tomato germplasm. Germplasm comprised of 82 accessions including accessions of Solanum lycopersicum L. and four wild species S. chilense, S. habrochaites, S. pennellii and S.pimpinellifolium. At morpho-physiological level data was recorded for qualitative and quantitative traits from seedling to reproductive stages in 2006 and 2007. F-ratio and heritability values were high for most of the traits. Cluster analysis revealed grouping of accessions based on similarities irrespective of geographical origin. Principal Component Analysis (PCA) revealed positive contribution of fruit traits on PC1 while vegetative and agronomic traits on PC2. Towards yield Correation studies revealed complex pattern of association. Path analysis revealed that direct selection of the genotypes with greater equatorial diameter or multiple trait selection for traits which exert indirect positive effects through fruit diameter may meet the target of yield improvement. The germplasm investigated had enough variation (>50%) which can be employed in future breeding programs for yield as well as other vital combinations. Keeping in view the results of path analysis and other statistics 19 accessions have been identified for yield enhancement program. Genetic variance of 82 genotypes was studied for seed protein profile also. Out of 23 bands one was monomorphic and 22 were polymorphic. Low polymorphism was detected and cultivar identification was not possible. Cluster analysis did not reveal differentiation either for agronomic traits or origin. In a representative sample of 39 accessions microsatellite analysis was performed employing 15 SSR markers. An average of 2.8 alleles per locus was observed. Average Polymorphism Information Content (PIC) value was 0.507. From the results it is concluded that SSR markers were effective in detecting polymorphism in crops with high genetic similarity. Regarding wild species S. pimpinellifolium was distinguishable while for rest of three species it seems pertinent to conclude these as cultivated tomato not the wild species.