Gomphonema apuncto lacks a stigma.
Gomphonema freesei has coarse striae.
Gomphonema amerhombicum is more clavate and larger in size.
Gomphoneis rhombicum has a stria density of 9.5-12 in 10 µm, length of 35-53 µm and width of 4.5-7.5 µm. Note that G. rhombicum has not been verified in North America.