The fragmentation dynamics of the hydrogen molecular ion H-2(+) and of its isotopic derivate HD+ subjected to an intense pulsed laser radiation are studied using quantum wave packet propagations, It is shown that bichromatic optical excitations are subject to a high degree of control through the variation of the relative phase between the two fields. A phase-locked (omega,2 omega) laser pulse is used to induce asymmetry in the angular distribution of the emitted fragments. In addition, an appreciable isotope separation in the fragmentation of HD+ is predicted. The critical role of quantum molecular interferences in such phase-controllable processes is demonstrated.