Using glass capillary gas chromatography (GC) and ion-pair reversed-phase high-performance liquid chromatography (HPLC), a pair of structurally similar microbicides, benzyl diisobutylphenoxyethoxyethyl dimethyl ammonium chloride and its cresoxy-analogue, were effectively resolved and accurately quantified with a high degree of selectivity and specificity. Optimization of conditions in the chromatographic systems to attain desirable baseline separations of the components of interest is described. The minimum detectable quantities as determined are in the neighborhood of 10 ng for the quaternary ammonium salts by HPLC-UV detection, 0.1 ng for the cyanamide derivatives of the salts by GC-alkaline flame-ionization detection and 1–2 pg for the trichloroethyl carbamate derivatives of the salts by GC-electron-capture detection. In conjunction with cation-exchange chromatography for sample enrichment and purification, the glass capillary GC and ion-pair reversed-phase HPLC methods presented here are particularly suitable to separate and simultaneously analyze for the aryloxyethoxyethyl benzyl dimethyl ammonium compounds concerned in environmental samples. It appears that these chromatographic techniques possess potential applicability to the separation and quantification of other classes of quaternary ammonium compounds with closely related structures that are not separable by other methods.