Navicula flatheadensis has larger valves with wider, weakly protracted apices. Proximal raphe ends of N. flatheadensis are more distant and deflected to the primary side of the valve. The central nodule of N. flatheadensis is typically asymmetric and convex on one side. Navicula pseudolanceolata has less attenuated apices and more distantly spaced proximal raphe ends than N. subconcentrica.
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