Three Gomphopleura taxa, G. frickei, G. poretzkiae and G. cf. nobilis were found in one sample of diatomite of Setana, an Early Miocene sediment, from Hokkaido, Japan. The three taxa were observed using light and scanning electron microscopies, and their characteristics of shape, size, external opening of areolae, axial area, apical spine, apical pore field, longtudinal lines and raphe were documented and are described herein. The differences among the three taxa: G. frickei has a mostly parallel center G. poretzkiae has an expanded center and G. cf. nobilis has almost isopolar, lanceolate valve. Furthermore, G. cf. nobilis usually lacks marginal ridges, external openings of areolae are straight slit-shaped and longitudinal lines are near the valve shoulder.