| Summary: | Abstract Background The Capparaceae family is commonly recognized as a caper, while Cleomaceae represents one of small flowering family within the order Brassicales. Earlier, Cleomaceae was included in the family Capparaceae; then, it was moved to a distinct family after DNA evidence. Variation in habits and a bewildering array of floral and fruit forms contributed to making Capparaceae a “trash-basket” family in which many unrelated plants were placed. Indeed, family Capparaceae and Cleomaceae are in clear need of more detailed systematic revision. Results Here, in the present study, the morphological characteristics and the ecological distribution as well as the genetic diversity analysis among the twelve species of both Capparaceae and Cleomaceae have been determined. The genetic analysis has been checked using 15 ISSR, 30 SRAP, and 18 ISTR to assess the systematic knots between the two families. In order to detect the molecular phylogeny, a comparative analysis of the three markers was performed based on the exposure of discriminating capacity, efficiency, and phylogenetic heatmap. Our results indicated that there is a morphological and ecological variation between the two families. Moreover, the molecular analysis confirmed that ISTR followed by SRAP markers has superior discriminating capacity for describing the genetic diversity and is able to simultaneously distinguish many polymorphic markers per reaction. Indeed, both the PCA and HCA data have drawn a successful annotation relationship in Capparaceae and Cleome species to evaluate whether the specific group sort individual or overlap groups. Conclusion The outcomes of the morphological and ecological characterization along with the genetic diversity indicated an insight solution thorny interspecies in Cleome and Gynandropsis genera as a distinct family (Cleomaceae) and the other genera (Capparis, Cadaba, Boscia, and Maerua) as Capparaceae. Finally, we recommended further studies to elucidate the systematic position of Dipterygium glaucum.
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