A simple, two-layer theory of the atmospheric flow over an isolated mountain in two-dimensions (x-z) is developed to investigate how the boundary layer may effect mountain forced gravity waves. The model consists of a neutrally buoyant lower layer in which non-hydrostatic effects are retained and an upper layer with constant static stability where the hydrostatic approximation is imposed. The basic state wind is considered constant in the upper layer, and constant or linearly sheared in the lower layer. The model is solved analytically and is compared to the classical inviscid, single layer solution for hydrostatic flow over a bell shaped mountain with constant basic state wind and stability. Compared to the single layer model there is a reduction in amplitude and vertical flux of horizontal momentum in the propagating gravity wave field in the upper layer. Perturbation quantities decay with height in the lower boundary layer due to the dynamical influence of the neutral stratification in this layer. Two non-dimensional parameters control the reduction in wave amplitude in the upper layer. These are the ratio of the mountain half width to the boundary layer depth, and the ratio of the surface windspeed to the windspeed at the top of the boundary layer.