Eunotia lewisii can be most easily distinguished from similar species, including E. pienitzii, E. lapponica, and E. macroglossa, by its extremely prominent helictoglossae and the thickened silica ridge that continues from the helictoglossa to the dorsal margin. Eunotia lewisii most closely resembles E. pienitzii, but can be distinguished by its greater length and width and its slightly increased and more regular stria density. Eunotia lapponica can be distinguished by its broader and more variable valve width and its often convex dorsal margin, as well as the curved distal raphe ends that terminate closer to the apices. Eunotia macroglossa differs by a shorter valve length and decreased stria density, convex dorsal margin, and the absence of the thickened ridge from the helictoglossa to the dorsal margin.