Molecular dynamics simulations of flow between concentric rotating cylinders are performed. As the relative speed between the two cylinders is increased, a spontaneous flow bifurcation occurs and vortices form in a stationary-vortex or traveling-wavy-vortex configuration. The former emerges when the axial boundary conditions constrain the flow by reflection, and the traveling-wavy-vortex flow develops when the axial boundaries are relaxed to periodic conditions. The flow bifurcation is triggered by the thermal fluctuations in the system, and the resulting flow field is in agreement with previous experimental observations. In addition, the temporal growth of the Fourier mode that characterizes the wavy-vortex motion is well described by Landau's theory for Hopf bifurcations. The spatiotemporal energy spectrum is evaluated in order to characterize the instability in terms of its azimuthal wave number and wave speed.