Animal identification is a very vital issue in both genetic and forensic fields. Mitochondrial DNA (mtDNA) analysis has been often used to explore haplotype variety among and within animal species. The mtDNA displacement-loop (D-loop) region is highly variable than other DNA regions and it is regularly utilized to investigate the phylogeny of highly correlated breeds within species. In this investigation, the mtDNA D-loop sequence was analyzed to evaluate the genetic diversity and origin of four Egyptian sheep breeds (Ossimi, Baladi, Rahmani, and Barki). Additionally, phylogenetic analysis was performed through alignment of the obtained sequences with those available in the GenBank database (goat, pig, buffalo, horse, donkey, and dog). Sequence analysis of the mtDNA D-loop revealed a clustering of the Ossimi and Baladi sheep breeds (haplotype A), while the Rahmani and Barki sheep were observed to cluster (haplotype B). The pairwise differences among the four Egyptian sheep breeds and other sequences indicated a high genetic distance from the dog and the maximum identity was clearly established with goat and pig. In conclusion, this information can help to authenticate sheep species from other taxa and identify the origin of meat of commonly consumed species (cattle, buffalo, goat, and pig) and commonly banned species (dog, horse, and donkey) for food control and forensic purposes.