Seabird populations experience predation that can impact their breeding density and breeding success. The Cape gannet Morus capensis is endemic to the Benguela upwelling ecosystem and is classified as Endangered by the IUCN. They are affected by several threats, including predation by the Cape fur seal Arctocephalus pusillus pusillus. Many fledglings succumb to predation during their maiden flight across waters around the island. To curb predation, the selective culling of individual predatory seals was implemented in 2014, 2015, and 2018. Our first study objective was to determine if selective culling of Cape fur seals significantly reduced predation probability on Cape gannets. We tested whether predation probability in 2014, 2015, and 2018 was affected by fish biomass, gannet fledgling numbers, and/or the presence/absence of selective culling. Our second objective was to determine what led to fluctuations in Cape fur seal predation on Cape gannet fledglings between 2007 and 2018. We tested whether fish biomass and the amount of Cape gannet fledglings in the water affected predation probability on the fledglings. Results indicated that selective culling reduced predation within years. We found that with both increased fledgling numbers and increased fish biomass, seal predation probability was reduced. This suggests that a sustainable way to promote the conservation of Cape gannets would be to increase food availability for both the Cape fur seals and Cape gannets. Our findings, collectively with the global trend of the declining Cape gannet population and their endemism, provide reasons advocating for the conservation of the food resources of both the Cape fur seal and the Cape gannet in the Benguela system.