More than 1000 individual marine islands and islets occur within 2000km of the African shoreline. The location, size, and degree of isolation make many of these islands ecologically and culturally unique. However, these same characteristics also make these islands fragile and vulnerable. We define the concept of “mountain islands” through an arbitrary definition of elevation >1000m above sea level, resulting in 16 such islands scattered in seven archipelagos. All 16 islands—together with the archipelagos in which they occur—harbor unique and irreplaceable ecosystems and biodiversity. However, all have threatened ecosystems from direct human impacts (e.g., deforestation and human-initiated fires) and invasive species encroachment; these challenges are being amplified by climate change. To mitigate some of these threats, a number of management initiatives and programs are being implemented on various islands—some with great success. One such success story is the biological control of the invasive Giant Bramble Rubus alceifolius on La Réunion, and reforestation programs of the almost extinct lowland dry forest on the same island. Risks to people and livelihoods on many of the islands are caused by volcanic hazards (such as La Palma and Grande Comore, in the Canaries and Comoros), and from floods and mass wasting (e.g., landslides) during seasonal cyclones (such as on La Réunion, in the Mascarenes). Further interdisciplinary research—and a strong social sciences component—is needed to further understand social-ecological dynamics on such islands: these include reducing tensions between livelihoods and the control of invasive species, restoration programs and fire management, and expanding monitoring capabilities to manage risks from volcanoes and cyclones. Building island resilience against climate change shocks would be a common thread in such research—including enhancing endemic ecosystem resilience. Stronger science relationships between island-based academics and African continental counterparts can increase co-learning on topics such as fire studies/management, invasive species, mountain ecosystem management, and social-ecological studies under global change.