Abstract: Penguins are important top consumers in marine food webs and are one of the most threatened bird families, especially by climate change and food web alterations by marine fisheries. Yet, long-term population trends are lacking or are uncertain for many populations. Seven species of penguins breeding at the French Southern Territories in the southern Indian Ocean on the Crozet, Kerguelen, Saint-Paul–Amsterdam archipelagos and in Terre Adélie/Adelie Land, Antarctica are monitored regularly. This monitoring started in the early 1950s and most populations have been surveyed during the past four years, allowing assessments of population trends. King penguins increased at nearly all breeding sites within the Crozet and Kerguelen archipelagos. Emperor penguins have decreased at Terre Adélie/Adelie Land, with a partial recovery of the colony during the 2010s. Gentoo penguin populations at Crozet and Kerguelen are highly variable but stable. Adélie penguins have been increasing in Terre Adélie/Adelie Land. The trends in eastern rockhopper penguins vary between colonies and archipelagos. Northern rockhopper penguins have continuously decreased in numbers at Amsterdam Island, but appear to have increased at the nearby Saint-Paul Island. Macaroni penguins have first increased and then stabilized since the 2000s at Kerguelen and are stable at the Crozet Islands. Overall, most penguin populations breeding in the French Southern Territories increased or were stable over the past 30–60 years, with the exception of the northern rockhopper penguin, king and gentoo penguins on Crozet and the emperor penguin. The ecological reasons for these trends are poorly understood and require further investigation.