As-grown and post growth annealed pseudomorphic ZnSe epilayers grown on GaAs (001) by molecular beam epitaxy (MBE) in a single chamber have been studied by transmission electron microscopy (TEM). The density of stacking faults in as-grown layers can be reduced by three orders of magnitude when growth is initiated on a 2x3 reconstructed surface instead of the usual 2x1 reconstruction. There is also a correlation between the misfit dislocation configuration in post growth annealed pseudomorphic layers and the substrate reconstruction. Epilayers grown on 2x1 reconstructed substrate are dominated by zig-zag misfit dislocations deviating from the orthogonal directions while straight orthogonal misfit dislocations dominate in epilayers grown on 2x3 reconstructed substrate.