late 15c., from ear (n.1) + mark (n.1). Originally a cut or mark in the ear of sheep and cattle, serving as a sign of ownership (also a punishment of certain criminals); first recorded 1570s in figurative sense "stamp of ownership."
1590s, "to identify by an earmark," from earmark (n.). Meaning "to set aside money for a special purpose" is attested by 1868. Related: Earmarked; earmarking.