Cyclotella atomus is smaller (valves < 8.5 µm in diameter) lacks spines, and marginal fultoportulae are distinct and extend beyond the valve margin.
Cyclotella cryptica has coarse striae (6-10 striae in 10 µm).
Cyclotella operculata has narrow tapering striae and the valve face is strongly undulate.
Stephanocyclus gamma has coarse striae (5-9 striae in 10 µm) and the valve is strongly transversely undulate.