We study three dimensional (3D) oceanic Lagrangian coherent structures (LCSs) in the Benguela upwelling region obtained from an output of the regional ocean modeling system (ROMS). To do that, we first computed finite-size Lyapunov exponent (FSLE) fields in the region volume that characterize mesoscale stirring and mixing. Average FSLE values generally decreased with depth, but there was a local maximum at a depth of approximately 100 m. LCSs are extracted as the ridges of the calculated FSLE fields. They present a “curtain-like” geometry in which the strongest attracting and repelling structures appear as quasivertical surfaces. LCSs around a particular cyclonic eddy, pinched off from the upwelling front, are also calculated. The LCSs are confirmed to provide pathways and barriers to transport into and out of the eddy.