Originally: a fly, especially one that bites or is troublesome to dogs. Now (US): specifically the stable fly, Stomoxys calcitrans.
Late Middle English; earliest use found in Medulla Grammatice. From dog + fly, chiefly after post-classical Latin cynomyia and its etymon ancient Greek κυνάμυια (in Hellenistic Greek κυνόμυια), used in ancient Greek (Homer) as a term of abuse and in Hellenistic Greek (Septuagint, etc.) with reference to one of the plagues of Egypt.