The measurement of heavy quark collective motion in heavy ion collisions is a powerful tool to reveal key QGP properties, such as shear viscosity and quark diffusion. PHENIX has new measurements of the second Fourier harmonic, $v_{2}$, of separated charm and bottom quarks at mid-rapidity $|$y$|$ $<$ 0.35 in Au+Au collisions at $\sqrt{s_{NN}}$ = 200 GeV. The technique utilized in these measurements makes use of the distance of the closest approach of electrons from the semi-leptonic decays of charm and bottom hadrons. In addition, measurements of $v_{2}$ of inclusive heavy flavor particles were performed in the small $d+$Au system using muon decays at forward and backward rapidities covering the range 1.2 $<$ $|$y$|$ $<$ 2.2. The experimental study in small systems will help the understanding of the origins of particle collectivity in hadronic collisions. This presentation will show these results and discuss them in the view of the current theoretical calculations.