This research aimed to validate new techniques in shark classification and perform a direct comparison to provide the best methodology to remove the boundaries against correct shark classification. The phenotype morphometrics of the dorsal and pectoral fins of two shark species (Carcharhinus falciformis and Carcharhinus plumbeus), inhabiting the Egyptian Red Sea water were investigated in comparison to the genetic identification through barcoding of COI from mitochondrial DNA. The results showed that phenotype morphometrics of the pectoral fins were better than dorsal fin morphometrics in differentiating between these shark species (C. falciformis and C. plumbeus). Condensed with previous results, DNA barcoding successfully features both species and clearly eliminates any confusion in their taxonomy. When the comparison level was raised across both species, pairwise distances significantly increased. COI gene sequencing produced an accurate method for unambiguous Egyptian Red Sea shark species differentiation. This might greatly help the active conservation and management efforts of those species in Egypt and throughout the world.