Two specimens of Calyptogena collected by the submersible Shinkai-2000 from Ryuyo Submarine Canyon of the Nankai Trough off the Pacific coast of middle Honshu (Tokai Region) are new to science. This species is characterized by solid, elongate oval shell that is ornamented by distinct concentric ribs, strong cardinal armature, and unusually distinct and deep pit for anterior pedal retractor scar beneath the anterior lateral tooth.