The genus Chironomus is one of the most important taxa of benthic macroinvertebrates in Japan. C. plumosus or C. nipponensis, C. flaviplumus and C. yoshimatsui are dominant species in muddy lake profundals, lake littorals and polluted rivers, respectively. In Japan, more than 20 Chironomus species are recorded, but their closely-similar morphologies have often caused problematic identifications. Therefore, accurate species-identification measures with the assistance of molecular phylogenetics is urgently needed. In this study, the phylogenetic relationships among several species of the genus Chironomus have been investigated using DNA sequences from a cytochrome c oxidase subunit I gene (COI). The analysis mostly supports the conventional phylogeny based on morphological analyses. A few important species have been compared in detail. For example, Japanese Chironomus "plumosus" appeared to be C. borokensis or the conspecific of European C. plumosus. Identity of Chironomus nipponensis, believed to adapt to a wide range of altitude from highland to lowland is under investigation.