The horn of Africa is endowed with two of the thirty three global hotspots: the Eastern Afromontane and the Horn of Africa. These are home for a large number of unique and characteristic plant and animal species that are huge potential resources for the livelihood of communities in the region. In addition these hotspots have huge potential for hydropower production that not only benefits particular countries, but that will empower Africa if used in a rational manner. However, there are challenges: anthropogenic factors, climate change, invasive species and inadequate capacity to implement even existing policies to address these challenges.