Abstract: Background and Objective: Haplophyllum tuberculatum is a valuable medicinal species with wide distribution in Mediterranean coastal desert of Egypt. It was characterized by high level of intraspecific morphological and biochemical variability. The objective of study was to assess the species status diversity for its coordinated conservation. Materials and Methods: Twenty-seven Operation Taxonomic Units (OTU’s) from nine populations were collected along the Mediterranean coastal desert of Egypt. Eighty seven macro and micro morphological characters, besides 114 molecular attributes from both seed storage proteins and RAPD were evaluated. The agglomerative cluster analysis conducted and the dissimilarity matrix analyzed through three sorting methods, average linkage UPGMA, single linkage and Ward's. Results: The OTU's from 19-21 of Abo-Tamr village were discriminated from the other populations due to a large distance between the inflorescence and the first leaf, united sepals and united stamens at base. The studied samples achieved 8 common bands and both El-Karma (OTU's 7-9) and El-Gophera villages were distinguished by the absence of both polymorphism and the band at 77 KDa. The discrete DNA products per primer ranged from 12-19 bands, the percentage of polymorphism from 24-31% and fingerprinting bands from 1-4. Conclusion: Two biotypes of H. tuberculatum can be distinguished, OTU’s from 19-21 of Abo-Tamr and the other ecotypes. The determination of the rank of these biotypes needs the study of the morphologically similar H. blanche to confirm the presence of the two species.