PHENIX has measured $J/\psi$ production at backward, central and forward rapidities both in p+p and d+Au collisions at $\sqrt{s_{NN}}=200$ GeV during the third run of the RHIC collider. From the p+p collisions, we measure the total J/$\psi$ cross section. From the d+Au collisions, we compute the nuclear modification factor versus transverse momentum, rapidity and centrality. All results presented here are preliminary.