Toxaphene is considered to be a problematic organochlorine pollutant because of its bioaccumulation potential and persistence in aquatic environments. In this study, whole lake trout and walleye composites were used to evaluate two analytical techniques for total toxaphene and selected congener analysis. The efficacy of using gas chromatography electron ionization tandem mass spectrometry (GC-EI/MS/MS) and electron capture negative ionization mass spectrometry (GC-ECNI-MS) were compared. Although the sensitivity using GC-ECNI-MS was approximately five times greater than GC-EI/MS/MS, the latter provided more consistent inter-Parlar relative response factors (RRF). When using technical calibration mixtures, these results suggest a more accurate total toxaphene measurement was obtained using the GC-EI/MS/MS method. Total toxaphene concentrations in lake trout composites from both methods were highly correlated (R(2) = 0.985) with the MS/MS concentrations approximately half of those determined by ECNI, suggesting systematic high bias in toxaphene concentrations when measured using GC-ECNI.