Pantocsekiella rossii has uniform striae ends near the central area, rows of areolae in the central area, and lacks papillae.
Pantocsekiella polymorpha has larger valves (greater than 8 µm) resembling P. rossii and small valves (less than 8 µm) resembling P. ocellata. Because of the variation in morphology with size, special attention should be given to examine full size range to make a correct identification.
Pantocsekiella kuetzingiana has more frequently branching striae, striae more often bundled in pseudosectors and greater irregularity in the striae ends.
Pantocsekiella comensis has a tangentially undulate valve face.