Simulium (Gomphostilbia) omutaense Ogata & Sasa, 1954 is the only named species in the Simulium batoense species-group of the subgenus Gomphostilbia Enderlein recorded from Honshu and Kyushu, Japan. It represents the northernmost distribution of this species-group, of which most members are distributed in the Oriental region. This species, the only member of the Simulium omutaense subgroup, is unique among the seven subgroups of the S. batoense species-group by having the pupal gill with one long filament and seven short filaments, similar to the arrangement of the pupal gill filaments in the S. zonatum subgroup of the S. epistum species-group in the same subgenus. This species is fully redescribed based on adults, pupal exuviae and mature larvae, and is most similar to species of the S. decuplum subgroup, based on adult morphological characteristics, although the pupal gill of the latter subgroup is markedly different by having 10 or 12 short filaments. Its close relationship to the S. decuplum subgroup is supported by a DNA analysis using COI gene sequences, with genetic distances of 9.30–11.02%. On the other hand, genetic distances between S. (G.) omutaense and species of the S. zonatum subgroup were 16.32–16.93%. Our study shows that a similar arrangement of the pupal gills in two different species-groups, which is rarely seen, has evolved independently and its occurrence does not necessarily reflect phylogenetic relationships.