Encyonopsis bobmarshallensis and E. kutenaiorum have more linear valves, lower stria density, and larger central areas. Encyonopsis moseri is similar in size and shape but has only 23-25 striae in 10 µm. Encyonopsis perborealis can be distinguished from other small Encyonopsis species by its broadly rounded apices, from species of Achnanthidium by its biraphid frustules, and from other small naviculoid taxa by its asymmetric valves.