Genetic diversity among in vitro plant regeneration in cumin has been examined by molecular markers analysis (ISSR and SRAP markers). Two landraces of cumin named Egyptian landraces (EGY genotype) and Indian landraces (IND genotype) were used as donor parents, three types of explants (hypocotyl, cotyledon and root) and four MS tissue culture media with different concentrations of growth regulators (auxin and cytokinin) were used to study the impact of genotype, type of explants and growth regulators on callus formation and plant regeneration in cumin. Significant differences among two cumin landraces were observed for regeneration rate and number of shoots per explant. These differences were depending on genotype, explant type and concentration of growth regulators. The best regeneration medium (MS with 0.5 mg/L 2,4-D) used for establishment of regenerated plants. Donor parent, Egyptian landraces (EGY) and Indian landraces (IND) and its regenerated plants on regeneration medium were selected and subjected to somaclonal variation analysis using molecular markers. ISSR (inter- simple-sequence-repeat) and SRAP (sequence-related-amplified-polymorphism) markers were used to detect the genetic variations between two cumin landraces. Subsequently, primers which exhibited high polymorphism between donor parents were used to analysis of somaclonal variation between each donor parent and its regenerated plants (somaclones), as well as among somaclones. These markers revealed polymorphism showing clear different DNA fragment patterns in all somaclones, which were eminent in their differences from parents.