Genetic diversity during prebreeding or postbreeding programme, is the key pillar to characterize the valuable traits and gene of interest. Whereas, superior or inferior heterotic performance of F1 depend on the diverse nature of their pedigree. Therefore, the aim of this study was to see the diversity between the interspecific crosses and effect of heterosis, and inheritance for the morphological traits and ToLCV resistance. All the 24 F1 interspecific crosses were classified into four clusters on the basis of morphological traitsas well as simple sequence repeat (SSR) markers. Among the F1 hybrids, 23 were grouped into clusters II, III and IV with different phylogeny, while PBC×EC 521080 was individual with cluster I. On the basis of visual observation of fruit colour, deep red and green colours in the crosses of S. pimpinellifolium (EC 521080) and S. habrochaites (EC 520061) exhibited dominant effects. In context of heterosis breeding, the crosses which were made using Solanum pimpinellifolium (EC 521080), S. chmielewskii (EC 520049) and S.cerasiforme (EC 528372) were better for yield capacity and the crosses of S. habrochaites (EC 520061) exhibited low and negative heterosis for ToLCV resistance. The F1 progenies were segregated in various Mendelian ratio as follows 3:1, 1:2:1, 1:3, 13:3, 15:1, 12:3:1 and 9:6:1 for ToLCV disease reaction of incidence, plant growth habit and fruit colour appearance, respectively. Therefore, these interspecific crosses can be utilized for developing high yield, impressive fruit colour combiners and resistant hybrids/varieties of tomato.