Gomphonema caperatum has shorter, more narrow valves, and a more broadly lanceolate axial area. 
Gomphonema christenseni lacks a stigmoid and the headpole end is more tapered. 
Gomphonema incognitum is smaller in both length and width. 
Gomphonema insularum has shorter, more narrow valves, a more broadly lanceolate axial area that does not expand into a defined central area and a sinuous raphe. 
Gomphonema stoermeri has shorter, more narrow valves, a narrower axial area, and a smaller central area. 
Gomphonema amerhombicum has more finely spaced striae (>14 in 10 µm) and the footpole has somewhat concave margins.

LM scalebar = 10 µm
Length Range
35.0-53.9 µm
Width Range
6.5-7.5 µm
Striae in 10 µm
12.1-14.5 at valve center, 14.2-16.2 at headpole, 11.7-15.4 at footpole
Gc53921  Gomphonema Freesei 1
Gc53921  Gomphonema Freesei 2
Gc53921  Gomphonema Freesei 3
Gc53921  Gomphonema Freesei 4 Holotype
Gc53921  Gomphonema Freesei 4B Holotype
Gc53921  Gomphonema Freesei 5
Gc53921  Gomphonema Freesei 1 Gc53921  Gomphonema Freesei 2 Gc53921  Gomphonema Freesei 3 Gc53921  Gomphonema Freesei 4 Holotype Gc53921  Gomphonema Freesei 4B Holotype Gc53921  Gomphonema Freesei 5

Gomphonema caperatum

Ponader and Potapova 2017

Length Range
22.4-31.9 µm
Width Range
4.4-5.2 µm
Striae in 10 µm
14-16
Gomphonema caperatum LM3 Gomphonema caperatum LM7 Gomphonema caperatum LM4 Gomphonema caperatum LM2 Gomphonema caperatum LM1 Gomphonema caperatum LM5 Gomphonema caperatum LM6

Gomphonema christensenii

R.L.Lowe and Kociolek 1984

Length Range
32.8-57.4 µm
Width Range
6.1-7.8 µm
Striae in 10 µm
13-16
Gomphonema christenseni LM2 Gomphonema christenseni LM5 Gomphonema christenseni LM6 4 53920  Gchristenseni Holo 5 53920  Gchristenseni2 6 53920  Gchristenseni2 7 53920  Gchristenseni2

Gomphonema incognitum

E.Reichardt, Jüttner and E.J.Cox 2004

Length Range
17.8-29.5 µm
Width Range
5.0-5.8 µm
Striae in 10 µm
13-16 at mid-valve; up to 18 at the apices
G Incog 15620A 10132015 12 Cl G Incog 15576A 08142015 20 Cl G Incog 15576A 08142015 37 Cl G Incog 15576A 08142015 21 Cl G Incog 15558A 08132015 42 Cl G Incog 15576A 08142015 29 Cl G Incognito Lm6

Gomphonema insularum

Kociolek, Woodward and Graeff 2016

Length Range
15.2-42 µm
Width Range
4.4-7 µm
Striae in 10 µm
13-16
Gomphonema insularum LM1 Gomphonema insularum LM2 Gomphonema insularum LM3 Gomphonema insularum LM4 Gomphonema insularum LM5 Gomphonema insularum LM6 Gomphonema insularum LM7

Gomphonema stoermeri

Kociolek and Kingston 1999

Length Range
19-45 µm
Width Range
4-6 µm
Striae in 10 µm
13-15
Gomphonema stoermeri LM7 Gomphonema stoermeri LM2 Gomphonema stoermeri LM3 Gomphonema stoermeri LM5 Gomphonema stoermeri LM1

Gomphonema amerhombicum

E.Reichardt 2007

Length Range
22.5-60 µm
Width Range
5.6-7.7 µm
Striae in 10 µm
13-15 at mid-valve, up to 17 at headpole
G Amerhombicum  B Isotype 20170301 06 Cl G Amerhombicum  A Isotype 20170301 08 Cl G Amerhombicum  A Isotype 20170301 18 Cl G Amerhombicum  B Isotype 20170301 05 Cl G Amerhombicum  B Isotype 20170301 14 Cl G Amerhombicum  B Isotype 20170301 09 Cl G Amerhombicum  B Isotype 20170301 21 Cl