Abstract: Background and Objective: Genetic characterization for seed heterospermy (seed shape, seed size and seed color) has been studied based on cytological (chromosome number), molecular markers (RAPD, ISSR and SCoT) and morphological study. The aim of this study was to clarify the genetic diversity characterization in 6 Egyptian taxa characterized by heterospermy i.e., seed polymorphism either seed shape, seed size and seed color polymorphism. Materials and Methods: Seeds and young leaves of three groups: seed shape polymorphism (Emex spinosa and Limbarda crithmoides), seed size polymorphism (Cakile martima and Raphanus raphanistrum) and seed color polymorphism (Chenopodium murale and Urospermum picroides) were collected from their natural habitats in Egypt. Seeds were used for metaphase chromosome number after fixation and squashing steps. Molecular markers RAPD, ISSR and SCoT were used by five primers for each marker. Results: In this study chromosome number for Emexspinosa 2n = 20, Limbarda crithmoides 2n = 18, Cakilemartima 2n = 18, Raphanus raphanistrum 2n = 18, Chenopodiummurale 2n = 18 and 2n = 10 for Urospermum picroides were found. RAPD, ISSR and SCoT molecular markers generated a total 492 total bands with 130 polymorphic bands and 362 common bands. RAPD marker was efficient to differentiate among studied taxa giving high polymorphism 33.96%. Scanning Electron Microscope (SEM) had the ability to compare between 2 seeds for the same plant giving different appearance in seed coat. Conclusion: Seed heterospermy not differ in chromosome number but differed in chromosome structure. In addition, it differed genetically that appeared in using molecular markers and scanning electron microscope. This attributes have the ability to conserve genetic diversity among species and can be used in the conservation of these species in gene banks.