Several Cymbella species are superficially similar to E. hamsherae (incluing C. affinis, C. affiniformis, C. excisa and C. exigua). Note that distal raphe ends are ventrally deflected in Encyonema and dorsally deflected in Cymbella. Furthermore, E. hamsherae lacks a stigma and has a straight, rather than a lateral raphe. In addition, the stria density is generally higher in E. hamsherae than in these Cymbella taxa.