In the last 15 years new research findings have radically reshaped our understanding of human effects on ocean ecosystems. Here I describe five major shifts in perspective that reveal our impacts to be more severe and persistent than previously appreciated. Firstly, scientists have delved deep into the past and found that the global expansion of European nations across the planet caused the large-scale loss of marine megafauna. In the past century, expansion of industrial scale fishing has continued the process, massively reducing the biomass of exploited species. Secondly, once depleted we are finding that populations rarely rebound rapidly, contrary to a widespread belief in greater resilience of marine compared to terrestrial species. Thirdly, marine ecosystems are being shifted into alternative states that are less desirable from the human perspective and may be stable. It could be difficult, or impossible in some cases, to reverse impacts once inflicted. Fourthly, marine species are at risk of extinction. Loss of shallow water marine habitats is proceeding as rapidly as on land, many species have small geographic ranges, and many possess life history characteristics that leave them highly susceptible to overexploitation. Finally, the deep sea is not beyond harm. Depletion of shallow water fisheries and technological advances are opening up the deep to exploitation and its collateral impacts. If we are to reverse these negative trends we must establish large-scale networks of marine reserves that are off limits to damaging activities and fishing. Such reserves would protect biodiversity, and recover and sustain the world's fisheries productivity.