Gypsy moth, an important forest/urban pest worldwide, is separated into the European and Asian subspecies, and has important quarantine significance. Diagnostic technique that can accurately and quickly distinguish subspecies is lacking. This study aimed to evaluate genetic difference between the subspecies, and subsequently to develop a reliable and high throughput molecular based diagnostic tool for distinguishing the subspecies. COI genes of 25 gypsy moth samples from China, Russia, Mongolia, Japan and the United States were sequenced. DNASTAR analysis revealed that gypsy moth COI gene was 1531bp long. The UPGM phylogenetic tree constructed based on the COI gene indicated that European subspecies (U.S. population) and Asian subspecies were distinctively divided into two branches. Japanese populations had a far distantly relationship with other Asian populations forming a separate branch. There was a single base substitution (base transformation only) at 14 consistent locations between Asian and American populations, but 13 of them coded the same amino acid. A MGB proper and TaqMan assay was designed base on the base substitution at 406th bp that coded a different amino acid. This allele typing assay took only 4 hours and could accurately distinguish gypsy moth subspecies of Europe and Asia. The study enriches the knowledge basis of genetic differentiation of gypsy moth subspecies. And more importantly the TaqMan assay is the first report of such diagnostic tool that could deliver rapid and accurate results and suitable for routine quarantine inspections to distinguish Asian and European gypsy moth subspecies. This study was supported by the Ministry of Science and Technology of the People’s Republic of China (Science and technology supporting project: 2012BAK11B03; International cooperation project: 2009DFA31950) and Jiangsu Entry and Exit Inspection and Quarantine Bureau (2014KJ45).