Burundi has made a great biodiversity conservation effort during the last 50 years. For the 11 legally recognized parks and protected areas covering 135139 ha; three of them have important water bodies and cover approximately 72742 ha. These include the Ruvubu National Park (RNP) with only 11 native fish species, the Rusizi National Park with 45 native species known from the whole basin where, however, results from a recent survey (2008-2010) show a very low recovery rate of the species reported in literature and in museum records; and finally the Bugesera Protected Aquatic Landscape with 12 native species currently known.The Upper Malagarazi River basin in Burundi which is not included in any legally protected area today is a particular case for the country. Once less inhabited, the Malagarazi valley currently has attracted many immigrants from highly populated provinces of Burundi and seasonal migrations for cattle pasture. Fishing there is mainly for subsistence and remains a secondarily activity after agriculture although a few people rely on it for their livelihood. With at least 75 native species the Upper Malagarazi is without any doubt, Burundi s main riverine fish hotspot. However, wetland conversion into cropland is dangerously increasing. It seems that the best and fastest way to save this aquatic biodiversity of the country is to support the current project of creation of the Malagarazi Natural Reserve. Based on the above mentioned species richness, we expect to stimulate a political awareness of the uniqueness of Burundi s fish biodiversity in that area and the need to protect it. The Malagarazi Reserve is a great opportunity to establish a framework for trans border collaboration with Tanzania to the protected areas level; interconnection of the Malagarazi Natural Reserve to the Malagarazi Muyowosi Game Reserve in Tanzania being the target with the consecutive benefit of faunal exchanges.