Achnanthidium duthiei differs from A. latecephalum and Achnanthes lineariformis by valve shape. While A. duthiei valves are linear to linear-lanceolate with capitate apices, A. latecephalum has linear-lanceolate valves with broadly rostrate or subcapitate ends, is smaller in size, and has a higher striae density. Achnanthes lineariformis has linear to linear-elliptical valves.