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Abstract The present study aimed to identify the molecular markers as well as the effects of genotype, explant and hormone balance on the ability of shoot regeneration in vitro tomato propagation. Six commercial cultivars (SM, UC97-3, CR, SQ, SSB and RS) and four hybrids (SM×CR, SSB×CR, RS×CR and SQ×CR) were used as different genotypes. Two explant types (shoot tip, eypocotyl) and three media composition (M1) (MS + BA 2 mg/l + Kin1 mg/l.), M2 (MS + BA 0.5mg/l + Kin0.5mg/l.), and M3 (MS + BA1 mg/l + Kin2 mg/l.)] affected shoot regeneration in all the tested genotypes. The (M1) of medium promoted the shoot tip explant to produce shoots. The hybrid SM×CR possessed high number of shoots.Ten ISSR primers were individually amplified to allow the differentiation of the materials under study. The evaluation of the dendrogram showed 79% similarity between SSB and UC97-3 cultivars and they are located in a separate group, and 82% similarity between CR, SQ, RS, SM cultivars. from the results obtained in this study, ISSR markers have a high efficiency to differentiate the tomato cultivars. Three primers i.e., 17899A, 17898A and 17898B may be used as a specific primers in tomato genotypes for discovery of molecular markers to high ability shoot regeneration genotypes |