A study was conducted to explore phenotypic variation in two Raphanus species: Raphanus raphanistrum and R. pugioniformis, which are found in the East-Mediterranean region. For each species, a 100m2 area representing their respective habitats was selected. Morphological characterization of the whole plant, leaves, and fruits was carried out in the field. The study analyzed morphological characteristics of R. pugioniformis populations during both flowering and maturity stages. It also compared the maturity stage characteristics. The examined characteristics included plant height, flower to plant ratio, leaf to plant ratio, leaf length, flower color, tip to pod ratio, seed to fruit ratio, fruit parameters (length, width, and weight), and the number of primary and secondary branches. Results revealed that plant height, tip to pod ratio, and fruit length increased from the flowering stage to the maturity stage. However, the number of primary and secondary branches and the ratio of seeds to fruit remained consistent between the flowering and maturity stages. R. raphanistrum exhibited greater plant height, flower to plant ratio, leaf to plant ratio, tip to pod ratio, seed to fruit ratio, fruit length, fruit width, fruit weight, and number of branches. The study examined also the dry weight and nitrogen, phosphorous, and potassium contents in leaves, stems, and seeds. It was found that R. pugioniformis had higher nitrogen and phosphorous contents in the leaves, stem, seeds, and whole plant compared to R. raphanistrum. R. pugioniformis exhibited higher nitrogen and phosphorous contents in the leaves, seeds, and whole plant. Similar trends were observed for potassium content. In summary, the study highlighted the phenotypic variation between R. raphanistrum and R. pugioniformis populations in the East-Mediterranean region. Differences were observed in various morphological characteristics, dry weight, and nutrient contents, providing valuable insights into the contrasting traits and adaptations of these closely related Raphanus species.