Charybdis natator is a portunid edible crab that is found in the Indo-Pacific, Indian Ocean, East Africa, and the Red Sea. The present study aimed to confirm the molecular identification of C. natator from the Red Sea using the DNA barcoding gene Cytochrome Oxidase Subunit I (COI). The molecular analysis was performed using genomic isolation from C. natator tissues followed by polymerase chain reaction (PCR) for the COI gene and sequencing. Data analysis was carried out using the Basic Local Alignment Search Tool (BLAST) and phylogenetic analysis conducted using the MEGA 6 program. The molecular identification of C. natator was confirmed and agreed with the morphological description. The phylogenetic analysis of genus Charybdis revealed that C. variegata (KJ168053 and KX018513) should be redefined as C. natator. The study supports promoting Goniosupradens to the generic level and negates its old morphological classification as a subgenus. It also suggests the re-evaluation of C. acuta taxonomical classification and emphasizes the significance of performing further molecular studies on other Charybdis species in order to resolve the misidentification and controversies.