In the present study, we add genetic data of the mayfly Cloeon dipterum collected from the Japanese Islands to the established molecular phylogenetic knowledge in the mitochondrial COI gene of Cloeon mayflies. Cloeon dipterum is a typical cosmopolitan species that includes six intraspecific haplotype groups. The present phylogenetic analysis revealed that haplotypes of the Japanese C. dipterum constitute a seventh group together with a haplotype from Korea. This East Asian group forms a sister group with previously known European and North American haplotype groups (i.e., the clade CT1 to CT3). The present phylogenetic analysis further revealed the occurrence of two described species (C. dipterum and Cloeon ryogokuensis) and possibly three species (Cloeon sp. 1 to 3) in Japan. Consideration is given to the degree of genetic differentiation, divergence time, and differentiation process among these seven genetic groups.