Indigenous and local knowledge (ILK) is increasingly recognized as a valuable asset in sustainability science. Knowledges of Indigenous peoples and local communities is becoming a critical tool for understanding coastal social-ecological systems and coping with global changes. The inclusion of ILK in research and management is key to local desirable social-ecological resilience and community-based conservation approaches, especially in areas with accelerated landscape changes. The Global South in particular is experiencing rapid changes through development and climate change, while harbouring many biodiversity hotspots. To synthesize the existing information and highlight still existing research gaps we conducted a systematic literature review on ILK from coastal ecosystems in the Global South (n = 254). Our results show to which biophysical aspects and ecosystems the knowledge is related, as well as the challenges and benefits that accompany the inclusion of ILK for management and research. Main challenges named were based on external forces, such as globalisation and market pressure but also a lack of integration and respect in governance and management for ILK and the difficulty of integrating ILK in today's academic work. Many researchers showed ways to overcome such multi-scale challenges and highlighted the importance of this process due to the various benefits of ILK for management and research. All articles reviewed named benefits in ecological (e.g. complementary knowledge production), political (e.g. support of community-based governance) or socio-cultural (e.g. maintenance of culture and livelihoods) aspects for management and research. Maintaining ILK is crucial for Indigenous people and local communities and carries insights to govern coastal ecosystems during the challenging times ahead. We conclude that future research is needed to further develop the current position of ILK in research and management of ecosystems, especially as global environmental changes may contribute to the acceleration of losing ILK from coastal ecosystems in the Global South.