The marine ecosystem provides numerous goods and services, dampens the impacts of floods and storms, and provides climate control, through the regulation of carbon fluxes, nutrient cycling, and the bioremediation of human waste and tourism. However, the ocean is vulnerable to anthropogenic threats and has been severely altered by humans.Seabirds and marine mammals are long lived, highly mobile, easily identifiable, and occupy the upper levels of trophic webs. These ecological features make them suitable as sentinels of the marine ecosystem.Sighting data collected during eight oceanographic surveys were analysed to describe and compare the biodiversity of the communities of top predators within the marine protected areas (MPAs) of Namuncurá/Burdwood Bank I and II and the surrounding areas in two contrasting seasons (summer and winter). Data were grouped into six zones based on depth and geographic position.Twenty‐five species of seabirds and 13 species of marine mammals were recorded in 113 days of surveys between 2014 and 2018. Top predator community composition varied seasonally in the different zones.A suite of indicator species was identified according to their specificity and fidelity to a particular zone. Most of the species identified as potentially useful indicators differed between summer and winter, highlighting the importance of conducting systematic surveys in both periods.The MPAs Namuncurá/Burdwood Bank I and II are key areas for top predator communities in the region, mainly in summer when the number and abundance of species increase. However, the waters around Isla de los Estados and the channel between Isla de los Estados and Burdwood Bank were also identified as a relevant habitat for many species. This knowledge should be included to create a regional network of areas under special management considerations that connect the established MPAs with other key pelagic and coastal areas (as found in this study) for the conservation of subantarctic marine megafauna. [ABSTRACT FROM AUTHOR]