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This is the first study of analyzing and identifying the hedgehog community in Egypt using a molecular marker especially it includes the Four-toed Hedgehog which is found in Gebel Elba but has never been signalized in Egypt. Thirty-two specimens are representing seven species and subspecies of hedgehogs were sampled. Five external measurements and eight cranial measurements were used. DNA was extracted and cytochrome b gene sequences data were analyzed. Maximum Likelihood tree based on Cyt b sequences reveals that there are two separate genetic clusters, one cluster for genus Atelerix and the other includes Hemiechinus and Paraechinus members. Genetic relationship between three subspecies of genus Paraechinus was detected, the morphological relationship was studied but there is a difficult to distinguish between them. These results strongly suggest that cytochrome b gene has been confirmed as an effective tool among mitochondrial genes, with high power of differentiation for species identification and characterization in both taxonomy and forensic science. [ABSTRACT FROM AUTHOR]