  Quarkonia provide a sensitive probe of the properties of the hot dense medium
created in high energy heavy ion collisions. Hard scattering processes result
in the production of heavy quark pairs that interact with the collision medium
during hadronization. These in medium interactions convey information about the
fundamental properties of the medium itself and can be used to examine the
modification of the QCD confining potential in the collision environment.
Baseline measurements from the d+Au and p+p collision systems can be used to
distinguish cold nuclear matter effects while measurements from heavy ion
collision systems, Au+Au and Cu+Cu, can be used to quantify in-medium effects.
PHENIX results for the production of the $J/\psi$ for a diverse set of
collision systems and energies and for the $\Upsilon$ in p+p collisions are
presented.
