The upper Malagarazi (uM) Basin is situated in Southeastern Burundi and Northwestern Tanzania, and partially covered by the Malagarazi Nature Reserve (MNR). A checklist of fishes from the uM, in Burundi, is presented based on a literature review, a re-examination of historical collections, and a study of new collections (2013 2022). A total of 74 native species, including 14 endemics and two introduced Oreochromis, distributed over 38 genera and 16 families, are reported. Of the aforementioned species, 60 native (81%) and one introduced are present in the MNR. The most important families in the uM and the MNR are the Cyprinidae (21 versus 17 species, respectively) and Cichlidae (12 versus 11). Other families are represented by less than 10 species in both the uM and the MNR. Furthermore, of the 14 species endemic to the uM (19%), only eight (57%) are reported from the MNR; the others are confined to some non-included affluent rivers. Moreover, eight taxa still await formal description. Finally, as some endemic and native species are not included within the current borders of the MNR, adjustments are proposed and the need for a new protected area is considered.