Changes in two contrasting ecosystems of the Benguela upwelling region, one dominated at mid-trophic level by jellyfishes (Namibia, northern Benguela ecosystem, where small pelagic fish abundance has been severely depleted) and one still dominated by small pelagic fishes (South Africa, southern Benguela) were compared in an effort to determine ecosystem trajectories under different exploitation regimes. The role of small pelagic fishes (clupeoids) was highlighted in the context of their importance in maintaining interactions in marine ecosystems. In particular, we examined trophic cascades and possible irreversible changes that promote the proliferation of jellyfishes in marine systems. We found that the presence of large populations of small pelagic fishes has a fundamental role in preserving beneficial trophic interactions in these marine ecosystems. The implications of trophic cascades, such as those observed in the northern Benguela, for ecosystem-based management were apparent. In addition, this comparison provides contrasting case studies to inform the development of management scenarios that avoid ecosystem shifts that affect predators and reduce the value of fisheries production.