Valves are heteropolar and flat, except for a depression at the head pole. The fibula density is 28-31 in 100 µm. The costae are short, while areolae and striae are delicate, which makes the valves appear structureless under LM. The raphe is positioned within a marginal canal, raised onto a keel, and supported by alar canals.
The large, flat, and structureless valves of Iconella guatimalensis are distinct and unlikely to be confused with any other diatom species.