A method of controlling protozoa trophozoite and cysts is disclosed, comprising administering a phosphonium salt of the formula: (R.sub.1).sub.3 P.sup.- R.sub.2.X.sup.-, wherein R.sub.1 is an alkyl group having from 1-8 carbons and R.sub.2 is a chain substituent having 6-20 carbons, 6514458