In 2004, two seismic reflection lines were shot across the Mesozoic Whitehorse trough and adjacent terranes. Three-dimensional first-arrival tomographic inversion is used to constrain lithology to 800–1200 m depth, and surface structures are extrapolated into the middle crust using the coincident reflection data. In the Yukon–Tanana terrane, the metasedimentary Snowcap assemblage is characterized by velocities of 4.5–5.5 km/s, while in Quesnellia, velocities of 5.0–6.0 km/s occur at 500 m depth, and probably represent igneous rocks of the Tatchun batholith. Across the Whitehorse trough, velocities >4.0 km/s correspond to clastic rocks of the Jurassic Laberge and Triassic Lewes River groups; velocities <4.0 km/s probably present the clastic Jurassic to Cretaceous Tantalus Formation. Several near-surface units with velocities of 2.0–3.0 km/s are identified; some correlate well with volcanic rocks of the Upper Cretaceous Carmacks Group, but others could be attributable to alluvial deposits or faulting. The Big Salmon fault is interpreted to dip southwest, implying that rocks of the Yukon–Tanana terrane extend beneath Quesnellia. Stikinia and Quesnellia underlie up to 5–8 km of Triassic to Early Cretaceous sedimentary strata, and appear to be a single allochthon within an 18–20 km deep synform above the Yukon–Tanana terrane, which we name the Northern Intermontane synform. In general, reflection geometries in the upper crust are complex, but are consistent with large-scale imbricate structures that have been dissected into numerous blocks by displacement along moderately to steeply dipping strike-slip faults, which may be part of a crustal-scale flower structure extending to the base of the crust.