The identity of Epidendrum sclerocladium, currently referable to Encyclia, is clarified with the recent collection of material unambiguously referable to this entity. In addition, we provide a new name in Encyclia for this taxon, E. rhizomatosa Tamayo-Cen, Carnevali & G.A.Romero, because the current combination, E. sclerocladia (Lindl. ex Rchb.f.) Hoehne, is based upon the later homonym Epidendrum sclerocladium Lindl. ex Rchb.f. This name is predated by Epidendrum sclerocladium Lindley as we argue that Lindley validly published the name in a horticultural catalogue, a nomenclatural issue herein discussed. Furthermore, because the vegetative portions of the plants were unknown until recently, we provide an epitype to supplement the holotype for the unequivocal identification of the species. A preliminary assessment of its conservation status and phylogenetic relationships are presented. Encyclia thrombodes is discussed and it is concluded that no known plants are referable to this entity at this time. A lectotype is proposed for Epidendrum cyperifolium because the holotype was destroyed. Finally, we provide an annotated checklist of the Encyclia species known to occur in Peru.