Achnanthidium crassum is difficult to distinguish, except under optimal illumination. Achnanthidium rivulare has a slightly smaller length-to-width ratio and parallel striae at the apices on the raphe valve. Achnanthidium deflexum has subrostrate ends, areolae that are resolvable in LM and shortened marginal striae in the center of the valve. Achnanthidium pyrenaicum has slightly rostrate ends and a fascia on the raphe valve.
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