The broadly lanceolate axial area is the best feature for differentiating F. pennsylvanica from species of similar size and outline. Fragilaria gracilis, F. rumpens, and Synedra famelica all have a straight, narrow axial area and valves are wider. Fragilaria rumpens and S. famelica have parallel striae. Synedra famelica has coarse areolae that can be resolved in LM. In SEM, F. gracilis has spines on the striae.