We focused on Meloe beetles that have lost all flight ability, and conducted molecular phylogeographic analyses based on their mitochondrial DNA COI and nuclear DNA EF1-α regions. Meloe beetles infiltrate bumblebee nests by attaching to bumblebees as they pollinate flowers and thereafter have a unique and specific life history as they complete their life-cycle within the host nest; flight-based dispersal is achieved by piggybacking on bumblebees. In fact, Meloe beetles, which cannot fly, even inhabit remote islands (i.e., “Oceanic Islands”). Regarding four species, i.e., Meloe coarctatus, Meloe proscarabaeus, Meloe violaceus and Meloe corvinus, the conventional morphological classification system based on morphological characteristics was strongly supported by the molecular markers. On the other hand, for two species, Meloe menoko and Meloe auriculatus, it was found that M. menoko may be evaluated as having a paraphyletic relationship with M. auriculatus. Furthermore, two other cryptic, undescribed species were also discovered in this study. One was collected in the Nikko Highland, and inhabited the area sympatrically with M. coarctatus. The other was collected from Hachijo-jima Island. These cryptic species were highly differentiated, independent lineages in terms of mitochondrial and nuclear gene regions. That is to say, a new level of species diversity was revealed among the Meloe beetle species, known for their unique and strange ecological and ethological characteristics.