Ceiba pentandra (L.) Gaertn. (kapok) (F: Bombacaceae) is a large, fast growing tree of up to 50 m height. It grows naturally in the tropical and subtropical regions of the world and planted as a shade tree. In traditional medicine, it is mainly used as an emetic, diuretic and antispasmodic agent. Extracts of different morphological parts of the plant has been also recommended for the treatment of various ailments, include diabetes, bronchitis, skin diseases, diarrhea, dysentery, eye diseases, arthritis, insect bite and chronic fever. There are at least four common varieties of Ceiba pentandra species include; var. caribaea (DC.) Bakh., var. guineensis (Schumach. & Thonn.) H. G. Baker, var. pentandra and var. indica Bakhuisen. However, there were no specific identification standards for such varieties in the previous researches. In this study, a detailed description for the morphological and anatomical characters of the leaves, stems and fruits of Ceiba pentandra var. pentandra is performed. Additionally, the DNA fingerprint of the variety pentandra was established to help in its future identification at the genomic level.