Freshwater habitats worldwide are experiencing many threats from environmental and anthropogenic sources, affecting biodiversity and ecosystem functioning. In Africa, particularly in Mediterranean climate zones, rapid human population growth is predicted to have great impact on natural habitats besides naturally occurring events such as unpredictable drought frequency and severity. Here, we analyze the potential correlation between odonate assemblage conservation priority (measured with the Dragonfly Biotic Index: DBI) and the magnitude of climate change and human perturbation in African regions with a dominant Mediterranean climate, namely Northern (NAR: Morocco, Algeria and Tunisia) and Southern African region (SAR: South Africa). Using a compilation of studies assessing odonate assemblages in lotic and lentic habitats of both regions (295 sites in NAR and 151 sites in SAR), we estimated DBI, temporal change in average annual temperature (T), annual precipitation (P), and human footprint index (HFI) in each site, then we tested whether sites with different levels of DBI were associated with different magnitudes of climatic and anthropogenic change. We estimated past (between 1980–1999 and 2000–2018) and future changes (between 1980–1999 and 2081–2100) in T and P based on three CMIP6 scenarios representing low (SSP126), moderate (SSP245), and high emission (SSP585), as well as the change in HFI from 1993 to 2009. We found that assemblages with higher DBI (i.e. higher conservation priority) encountered lower increase in T and slightly greater decrease in P than assemblages with lower DBI (i.e. lower conservation priority) in NAR during 1980–2018, but are projected to experience higher increase in T and lower decrease in P in future projections for 2081–2100. In SAR, the increase in T was mostly similar across assemblages but the decline in P was higher for assemblages with higher DBI during 1980–2018 and 2081–2100, suggesting that assemblages of higher conservation priority in SAR are threatened by drought. While HFI showed an overall increase in NAR but not in SAR, its temporal change showed only minor differences across assemblages with different DBI levels. We discuss the importance of management plans to mitigate the effects of climatic and anthropogenic threats, so improving conservation of odonate assemblages in these regions.