A highly sensitive and simple method for the analysis of chlorothalonil was presented using a liquid chromatograph/mass spectrometer equipped with an atmospheric pressure photoionization (APPI) source. Chlorothalonil is one of the most extensively used fungicides. The major degraded product of chlorothalonil, 4-hydroxy-2,5,6-trichloroisonaphthonitrile (4OH-TPN), was also quantified with sensitivity similar to that of chlorothalonil. The method was applied to the determination of chlorothalonil in aqueous environment and food samples. The method detection limits (MDLs) of chlorothalonil for aqueous samples and cucumber were determined to be 0.18 and 3.2 ng g(-1), respectively. At several estuarial locations, chlorothalonil was detected with a maximum of 1.1 ng L(-1). On the other hand, 4OH-TPN was detected not from estuaries but from rivers with a maximum of 14 ng L(-1).