The genetic structure of the Egyptian peach fruit fly (Bactrocera zonata (Saunders) (Diptera: Tephritidae)) population was analyzed using total RNA from adult females. A portion of mitochondrial cytochrome oxidase I (COI), 369 bp was amplified using RT-PCR, and was sequenced and analyzed to clarify the phylogenetic relationship of B. zonata established in Egypt. The data suggested that the gene shared a similarity in sequence compared to Bactrocera COI gene found in GenBank. Molecular phylogenetic analyses were performed based on nucleotide sequences in order to examine the position of the Egyptian population among many other species of fruit flies. The results indicate that four accession numbers of B. zonata (three from New Zealand and one from India) are closely related, while the Egyptian B. zonata are close to the 71 accession numbers of Bactrocera include one B. zonata from New Zealand. These two B. zonata from Egypt and New Zealand showed a close relationship in neighbor—joining analysis using the seven accession numbers of B. zonata. In addition, a theoretical restriction map of the homology portion of the COI gene was constructed using 212 restriction enzymes obtained from the restriction enzyme database to identify the Egyptian and New Zealand B. zonata.