Gomphoneis is very similar in shape to its sister genus Gomphonema.  It is asymmetrical over the transapical axis: in valve view its cells are wider at one end than the other, giving it a "club shaped" appearance.  In girdle view, it appears wedge shaped.  Gomphoneis is typically identified as distinct from Gomphonema by the presence of lines that seem to criss-cross the striae die to lined-up areolae.  However, some species, including G, olivaceum below, do not have these perpendicular lines.