The bird family Emberizidae contains around 300 seed-eating species, the majority of which are found in the Americas, although the genus Emberiza, with more than forty members, is confined to the Old World. Within its genus, the yellowhammer is most closely related to the pine bunting, with which it forms a superspecies; they have at times been considered as one species. The white-capped and cirl buntings are also near relatives of the species pair. Where their ranges meet, the yellowhammer and pine bunting interbreed; the yellowhammer is dominant, and the hybrid zone is moving further east.
The yellowhammer was described by Linnaeus in his Systema Naturae in 1758 under its current scientific name. Emberiza is derived from the Old German embritz, a bunting, and citrinella is the Italian for a small yellow bird. The English name is thought to have come from ammer, another German word for a bunting, and was first recorded in 1553 as yelambre.
There are three recognised subspecies. E. c. citrinella (Linnaeus, 1758), the nominate subspecies, occurs in southeast England and most of Europe east to the northwestern corner of Russia and western Ukraine, E. c. caliginosa (Clancey, 1940) is the form found in Ireland, the Isle of Man and Great Britain (except southeast England), and E. c. erythrogenys (Brehm, 1855) breeds from Russia, central Ukraine and the eastern Balkans eastwards to Siberia and northwest Mongolia, and also has isolated populations to the east of the Black Sea and in the Caucasus.