Several hydrophobic ionic liquids (ILs) based on long-chain aliphatic ammonium- and phosphonium cations and selected aromatic anions were analyzed by reversed-phase high-performance liquid chromatography (RP-HPLC) employing trifluoroacetic acid as ion-pairing additive to the acetonitrile-containing mobile phase and adopting a step-gradient elution mode. The coupling of charged aerosol detection (CAD) for the non-chromophoric aliphatic cations with diode array detection (DAD) for the aromatic anions allowed their simultaneous analysis in a set of new ILs derived from either tricaprylmethylammonium chloride (Aliquat 336) and trihexyltetradecylphosphonium chloride as precursors. Aliquat 336 is a mix of ammonium cations with distinct aliphatic chain lengths. In the course of the studies it turned out that CAD generates an identical detection response for all the distinct aliphatic cations. Due to lack of single component standards of the individual Aliquat 336 cation species, a unified calibration function was established for the quantitative analysis of the quaternary ammonium cations of the ILs. The developed method was validated according to ICH guidelines, which confirmed the validity of the unified calibration. The application of the method revealed molar ratios of cation to anion close to 1 indicating a quantitative exchange of the chloride ions of the precursors by the various aromatic anions in the course of the synthesis of new ILs. Anomalies of CAD observed for the detection of some aromatic anions (thiosalicylate and benzoate) are discussed.