Oncidium ornithorhynchum, an epiphytic orchid characterized by erect, pyramidal inflorescences and small yellow flowers, is found in the northern Andes. However, according to the protologue, the type was collected in Mexico during Humboldt and Bonpland's American expedition (1800–1804). To clarify this problem, we extracted DNA from the ancient holotype. Short‐range PCRs for plastid (matK‐trnK, trnH‐psbA, ycf1) and nuclear (nrITS) markers were established and used to infer its phylogenetic placement with several related Central American and Andean orchid species. This provided well‐supported and close relationships of the holotype with other North Andean orchids, proving that the locus classicus was confounded. Also O. sotoanum from Mexico, with which O. ornithorhynchum has often been confused, was only distantly related.