A new form of producing and sharing knowledge has emerged as an international (United States of America, Asia, and Europe) research collaboration, known as the Long-Term Ecological Research (LTER) Network. Although Africa boasts rich biodiversity, including endemic species, it lacks the long-term initiatives to underpin sustainable biodiversity managements. At present, climate change may exacerbate hunger and poverty concerns in addition to resulting in ecosystem degradation, land use change, and other threats in Africa. Therefore, ecosystem monitoring was suggested to understanding the effects of climate change and setting strategies to mitigate these changes. This paper aimed to investigate ecosystem monitoring ground sites and address their coverage gaps in Africa to provide a foundation for optimizing the African Ecosystem Research Network (AERN) ground sites. The geographic coordinates and characteristics of ground sites-based ecosystem monitoring were collected from various networks aligned with the LTER implementation in Africa. Additionally, climatic data and biodiversity distribution maps were retrieved from various sources. These data were used to assess the size of existing ground sites and the gaps in description, ecosystems and biomes. The results reveal that there were 1089 sites established by various networks. Among these sites, 30.5%, 27.5%, and 28.8% had no information of area, year of establishment, current status, respectively. However, 68.0% of them had an area equal to or greater than 1 km2. Sites were created progressively over the course of the years, with 68.9% being created from 2000 to 2005. To date, only 41.5% of the sites were operational. The sites were scattered across Africa, but they were concentrated in Eastern and Southern Africa. The unbalanced distribution pattern of the sites left Central and Northern Africa hardly covered, and many unique ecosystems in Central Africa were not included. To sustain these sites, the AERN should be based on operational sites, seeking secure funding by establishing multiple partnerships.