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In this article, I analysed the biogeographical distribution and the historical origin of freshwater fish of the Ethiopian Rift Valley (ERV) region which is not a homogeneous area. The Ethiopian region, including Eritrea and part of Somalia, includes 13 basins as geographical units. A comparison was carried out with four Near East geographical units. A correspondence analysis was applied to presence–absence data for the 17 basins × 170 species’ matrix. Then, a faunistic distance (Euclidian distance) between basins was computed from the coordinates of factors retained in this new analysis. From this faunistic distance, a hierarchical cluster analysis was performed and a dendrogram produced by a UGPMA classification. The old Abyssinian ichthyo-province (sensu Roberts, Zool J Linn Soc 57:249–319, ) was not homogeneous in species composition. I distinguished four main groups based on the present species composition which seemed to be mainly influenced by historical events. The species composition of the ERV basins was not randomly distributed and can be classified into four main geographical units. The importance of the historical events was demonstrated and two origins can be considered. The westernmost basins are under Nilo-Sudan influence whereas the easternmost ones seem to have been colonised from the Near East. In this Eastern part it can be distinguished three different groups: the main ERV province and two derived sub-regions, Lake Tana with a Labeobarbus intermedius related species flock and the Coastal Red Sea, characterised by a very impoverished freshwater fish fauna. [ABSTRACT FROM AUTHOR]