The response of a separated boundary layer to synthetic jet flow control at the global wake instability (F+ ≈ 𝒪(1)) and the shear-layer instability (F+ ≈ 𝒪(10)) measured by particle image velocimetry are presented. The visualization shows that in each of the control cases, coherent vorticity develops and breaks down into a turbulent wake. When the jets are actuated by burst-modulation at the wake instability frequency, they induce regular formation and detachment of large-scale vorticity to form a wide turbulent wake. Excitation at the shear-layer instability frequency, on the other hand, produces a train of alternating velocity fluctuations in the boundary layer which dissipate to a narrower wake. Proper orthogonal decomposition of the velocity fields show that the physical extent of the jet-induced coherent structures is decreased with increasing addition of momentum for both excitation frequencies.