We have theoretically studied the dissociation process of diatomic molecular ions submitted to an intense and short pulsed laser radiation. In order to control the dissociation dynamics, we have used the coherent control method, which is based on the superposition of two harmonics of the same laser with a constant phase shift. This creates quantum interference effects which are very sensitive to the value of the phase shift between the two colors, thus allowing a good control. We have performed a full non-perturbative wave packet propagation, which is equivalent to numerically solve the time-dependent Schrödinger equation. This approach allowed us to predict a selective control of the kinetic energy and the direction of emission of the photofragments. An application to the angular separation of the isotopes H+ and D+, which are emitted in opposite directions in the fragmentation of the HD+ molecular ion, is also presented.