A crucial menace for the biodiversity in arid and semi-arid territories is the global warming arising from anthropogenic activity. Egypt is expected to undergo an acute rainfall decrease and temperature boost in the next few decades, leading to many plant species' geographical allocation. Endemic plants of pleiotropic economic importance are strongly affected by climate change prospects, which will gradually result in losing our plant wealth genetic resources. Due to few studies on the Egyptian Brassicaceae family which has an economically and medicinally importance due to the presence of many active compounds that are included, in the pharmaceutical and cosmetic components (e.g., glucosinolates) besides having a large amount of antioxidant which inhibit the growth of microbes and also treat rheumatic diseases. The identification of this family still kind of fishy as researchers mostly relies on the morphological characters. To globally sustain this Egyptian plant family wealth's genetic pattern, it is substantial to characterize them based on their authenticated genetic background. Here we present a phylogenetic analysis of 16 species of the Egyptian Brassicaceae family using two plastid coding genes; Ribulose-1,5- bisphosphate carboxylase oxygenase (rbcL-a) and maturase K (matK). The maximum likelihood of the two markers for our samples was concordant with the Brassicaceae's references-sequences, which exist on plastid are considered highly conserved biomarkers. In conclusion, we have generated a robust phylogeny tree based on the molecular level that validates the Egyptian plant species and reliably differentiates them on morphological identification. This study is considered the first phase of Egyptian Brassicaceae family species authentication followed by biochemical studies serving the pharmacological and medicinal fields