As part of the LITHOPROBE Southern Cordilleran Transect investigations, twenty‐seven wideband magnetotelluric (MT) responses were obtained along 150 km of the reflection seismic lines. The MT profile begins to the east on the Rocky Mountain Trench above autochthonous North American basement, traverses across the Purcell anticlinorium, the Kootenay Arc, the Nelson batholith, and ends on the east side of the Valhalla gneiss complex. Sites near Kootenay Lake respond to a major near‐surface conductivity anomaly that is probably due to either graphitic schists or to an extension of the silver‐bearing mineralization found further north. The short period (<1 s) data from above the Nelson batholith indicate its thickness extent, whereas the long period (>1 s) data are highly complex and exhibit 3D regional features. Inversions of the data from the two sites on the Valhalla complex yield 1D models with interfaces in electrical conductivity at depths that agree with an increase in the number of reflectors at ≈9 km, “the base of layered reflections” at ≈22 km, and the Mono at ≈35 km. Of major significance to our understanding of the current composition and state of the lower continental crust is that although for the Valhalla complex there are few reflections below ≈22 km the MT responses indicate that the zone is conducting. This is the only location known to the authors where the lower crust is seismically transparent but electrically conductive.