Heavy quarkonia production is predicted to be sensitive to the formation of the quark gluon plasma in relativistic heavy ion collisions via competing mechanisms such as color screening and/or quark recombination. During 2004 and 2005 RHIC data taking periods, the PHENIX collaboration has measured J/ψ decay into lepton pairs both at mid and forward rapidity in Au+Au and Cu+Cu collisions at sNN=200GeV. We present the J/ψ nuclear modification factor and the J/ψ mean square transverse momentum as a function of the collision centrality for both systems, as well as the rapidity dependence of the J/ψ yield for different centrality classes. It is compared to different theoretical predictions. All Au+Au and Cu+Cu results shown here are preliminary.