Originally described as Troctes mesurus Cabanis and Heine (1863), with a type locality of Babahoyo, Ecuador. Apparently unaware of the name mesurus, Chapman later described this taxon as Curucujus melanurus pacificus (Chapman 1923), with a type locality of Alamor, Loja, Ecuador.
Most authors classified mesurus as a subspecies of Trogon melanurus (Black-tailed Trogon) (e.g., Peters 1945, Meyer de Schauensee 1966, Collar 2001). Ridgely and Greenfield (2001a) elevated mesurus to species status "based on its plumage differences (and also its striking pale iris), consistent vocal differences, and disjunct range". Phylogenetic analysis of DNA sequence data, from mitochondrial genes, confirms that mesurus and melanurus are separate species (DaCosta and Klicka 2008). Their results identify a clade that includes mesurus, melanurus, Trogon massena (Slaty-tailed Trogon), Trogon comptus (Blue-tailed Trogon), and Trogon clathratus (Lattice-tailed Trogon). Within this clade, clathratus is the basal species; melanurus is the sister to comptus, whereas the sister species to mesurus is massena (DaCosta and Klicka 2008).