common name of a strong-scented European plant long cultivated for its medicinal properties, c. 1300, camomille, from Old French camemile, from Late Latin camomilla, from Latin chamomilla, from Greek khamaimelon, etymologically "earth apple," from khamai "on the ground" (also "dwarf;" akin to khthōn "earth," from PIE root *dhghem- "earth") + mēlon "apple" (see malic). So called for its scent. Old English had it as camemalon.
Fowler (1927) writes that "Ca- is the literary & popular form; cha-, which represents the Latin & Greek spelling but has no chance of general acceptance, would be better abandoned in pharmacy also." But for once pessimism seems undue; British English kept the older spelling, American English favored the classically correct one, and on the internet the American spelling seems to have prevailed.