Encyonema lunatum is smaller in both length and width, and has broadly rounded ends. Encyonema neogracile is very similar, but is more narrow and smaller in length. Encyonema pseudogracile has a relatively broad axial area. Encyonema supergracile is the largest (length 54-74 µm, width 8.5-10.6 µm) of the E. gracile complex and was described from Columbia. Encyonema subgracile is smaller than E. pergracile, lacks a stigma and was described from Australia.