  The production of different quarkonium states provides unique insight to the
hot and cold nuclear matter effects in the strongly interacting medium that is
formed in high energy heavy ion collisions. While LHC explores the energy
frontier, RHIC has a broad physics program to explore the nuclear modification
at different energies in a wide range of systems. Some of the most interesting
recent results on $J/\psi$ and $\Upsilon$ production in p+p, d+Au and A+A
collisions from PHENIX and STAR are summarized in this work.
