Siyahoo mandarin (Citrus reticulata cv. Siyahoo) has been considered as one of the most well-known and popular cultivar of mandarin in Iran cultivated exclusively in Siyahoo district (Hormozgan province). Due to its special taste, texture and flavor it has been well received in the market. A new pest was found damaging mandarin fruits from this region which in the preliminary studied it was recognized as a lepidopteran larva. In the second year of incidence, 2017 we found a higher damage of the pest compared with the former year, indicating change in behavior of this pest to impose highly economic damage on mandarin fruits. In order to identify the pest taxonomically, samples of the infested fruits were collected and transferred to the plant protection laboratory of Hormozgan Agricultural and Natural Resources Research and Education Center. We used a molecular technique by employing DNA barcode for species identification. To do so, total genomic DNA of the larvae was extracted using CTAB methods and the Cytochrome Oxidase subunit I gene (COI) amplified using LCO 1490 and HCO 2198 primers. A positive PCR product was directly sequenced, edited and deposited in National Center for Biotechnology Information (NCBI) under MH460551 Accession number. Blast search of the ca. 700 bp of COI gene showed that this sequence shared 100% identity with sequence of Ectomyelois ceratoniae from family Pyralidae and subfamily Phycitinae (accession number: KF404735.1). Although, there are several reports regarding damage of E. ceratoniae on citrus species in other countries but this is the first report of E. ceratoniae damage on Citrus reticulata in Iran. This finding can be considered as a serious alarm regarding the possibility of changed behavior of this pest to be able to affect various citrus species all over the citrus growing areas of Iran.