Encyonema yellowstonianum has wider valves, but should be closely compared.
Encyonema kamtschaticum var. parvum valves are smaller, with a narrower axial area, and narrower central area.
Encyonema sinicum, E. reimeri, and E. temperei have larger valves, with a more gibbous ventral margin.
Encyonema nicafe has larger valves, with a more linear ventral margin.