The ornamental palms represent a diverse species in the national botanical gardens, and roadsides; however, the accurate identification of the palm trees (Arecaceae) is a problematic due to the numerous overlapped morphological traits, especially with the environmental conditions. So, the objective of this study was to implement the different morphological traits, especially based on the pyrene morphology, with the molecular barcoding markers of the plastid rbcL on delineation and revising the taxonomical identification of the most common Palm trees in Egypt in addition to their pharmacological and Ethnobotanical applications. An obvious variation on the surface of pyrenes among the studied Palm taxa ranged from ovoid to globose or discoid, with brown to pale brown, was recorded. The pyrene's fruit dimensions were ranged with S. yaba Becc. (5.65 × 6.85 mm), Washingtonia robusta (7.19 × 4.4 mm) and Sabal palmetto (Walter) Lodd. ex Schult. & Schult.f. (7.24 × 9.58 mm), while Syagrus romanzoffiana (Cham.) Glassman is (19.8 × 12.15 mm). The color of the pyrene of W. robusta, S. romanzoffiana, and Livistona decora (W.Bull) Dowe was brown, while was dark brown in Butia capitata (Mart.) Becc. Sabal yapa and S. palmetto. The SEM analysis of the pyrene surface microsculpture, the studied taxa of S. palmetto, S. yaba, Livistona, Brahea, and Sabal could be easily delimited at the generic level. The taxonomical identification of plant taxa based on their morphological characteristics, such as color, surface smoothness, and geometric shapes, was confirmed based on their molecular barcoding. The Principal Component Analysis (PCA) scatter plot based on the morphological traits distinguishes the taxa of tribe Cocoeae, subfamily Arecoideae and taxa of tribe Corypheae, subfamily Coryphoideae. From the UPGMA dendrogram based on the micromorphological characteristics, the studied taxa were grouped into two major clusters (I, II), the cluster I includes S. palmatto, S, yaba and W. robusta which belongs to subtribe Sabalinae, tribe corypheae, while cluster II includes L. decora, L. chinensis, (Jacq.) R.Br. ex Mart.and B. armata which belongs to subtribe Livistoninae and tribe Corypheae. Thus, the classification of the experimental plants based on the morphological traits of pyrene fruit microsculpturing was closely matched with the molecular barcoding based on the rbcL sequences.