Encyonema temperei has somewhat wider and more strongly dorsiventral valves and a more gibbous ventral margin where the central striae are about 1/3 the valve width.
Encyonema reimeri has somewhat wider and more strongly dorsiventral valves with acutely rounded apices.
Encyonema kamtschaticum and E. kamtschaticum var. parvum are smaller, with narrower apices and narrower axial and central areas.
Encyonema latum is much wider.
Encyonema nicafei and E. yellowstonianum are less dorsiventral, with flat or weakly convex ventral margins.