We developed a simple molecular detection tool that rapidly and accurately identifies Spotted wing Drosophila (SWD) without sophisticated instruments or expertise. We first identified a gene that is present in the SWD genome but not in that of any other insect species. Then, we developed the loop-mediated isothermal amplification (LAMP) assay, which was designed based on genomic DNA of SWD specific gene. This LAMP assay detected only genomic DNA from SWD—not from Drosophila melanogaster. In addition, this assay could detect genomic DNA in SWD geographical strains collected from 8 different locations in Asia, Europe, Hawaii, and the USA. Our LAMP assay could be a useful detection tool for identifying SWD rapidly in the field. This work was carried out with the support of the Cooperative Research Program for Agriculture Science & Technology Development (Project No: PJ0116302016).