In this work, the optimal control problems of the unsteady Navier-Stokes equations with variational multiscale stabilization (VMS) are considered. At first, the first order continuous optimality conditions are obtained. Since the adjoint equation of the Navier-Stokes problem is a convection diffusion type system, then the same stabilization is applied to it. Semi discrete a priori error estimates are obtained for the state, adjoint state and control variables. Crank Nicholson time discretization is used to get the fully discrete scheme. Numerical examples verify the theoretical findings and show the efficiency of the stabilization for higher Reynolds number. (C) 2015 Elsevier Inc. All rights reserved.