Knowledge regarding interactions between predators and their prey is fundamental for understanding underlying links between climate change and ecosystem responses, including predator demographics, in the Southern Ocean. This study reports data on reproductive performance, total population size and diet composition for macaroni and chinstrap penguins breeding at Nyrøysa on Bouvetøya during the summers of 1996–97, 1998–99, 2000–01 and 2007–08. The breeding populations of these two species at Nyrøysa decreased significantly over the study period, with an 80% decline for chinstraps and a 50% decline for macaroni penguins, despite relatively high levels of chick production. During this period macaroni penguins at this site ate a diverse diet, dominated by myctophid fish and two krill species, whereas chinstrap penguins were Antarctic krill specialists. The population changes are probably primarily due to the expanding Antarctic fur seal population, and also to landslides that are the result of increased melting on the island which have destroyed penguin breeding sites. Additional impacts from global warming of the ocean might also be playing a role and could exacerbate the decline in these penguin populations if krill and other prey are negatively impacted in the future in this region. The local chinstrap penguin population would probably be most heavily affected given its narrow feeding niche and small current population size.