Conservation of the endangered yellow-eyed penguin (Megadyptes antipodes) in New Zealand has principally sought to manage terrestrial threats, while relatively little has been done to understand or address marine threats, such as reduced prey availability, commercial fisheries interactions, and habitat destruction. We assessed spatial similarities between mainland yellow-eyed penguin marine distribution and resources (prey), risks (fisheries interactions), and areas of refugia (marine protected areas, MPAs). We determined if suitable penguin foraging habitat, based on environmental predictors using a Maxent species distribution model (SDM), also supports a high diversity of key prey species identified using a stacked SDM. We also created a novel index to predict areas of potential commercial fisheries interactions and mapped the overlap of penguin distribution and MPAs. Areas along the middle of the continental shelf had the highest prey diversity and probability of penguin presence, which overlapped with gillnet fisheries in these regions. Suitable penguin habitat also overlaps with trawl fisheries inshore along much of the South Island coast. <1 % of the penguin range overlaps with current MPAs, and the proposed South-East Marine Protected Areas network would protect only 3.6 % of the current penguin foraging distribution. This study takes an ecosystem approach to assess complex interactions between commercial fisheries, marine ecosystems, and MPAs, which is urgently required for marine spatial planning and adaptive ecosystem management of not only this endangered seabird but for southeast New Zealand coastal habitat and biota also.