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Genetic surveys of the endemic Padanian barbel Barbus plebejus (Osteichthyes: Cyprinidae) were completed on the lowland Adda River, a heavily regulated Italian Alpine river in which the European Barbus barbus is invasive. Both Barbus species are of the large fluvio-lacustrine ecophenotype and thus they share habitats in the river. Mitochondrial (N = 35) and nuclear (N = 256) DNA sequences were completed with the aim of estimating the extent and genetic consequences of the B. barbus invasion. The phylogenetic analyses, based on cyt b mtDNA, S7 ribosomal protein and growth hormone (GH) nuclear genes, revealed 59 haplotypes as B. plebejus and 37 as B. barbus. Genetic diversity values (H and π) and the mismatch distribution analyses indicated B. plebejus was still experiencing demographic radiation from a modest number of founders. The B. barbus cyt b haplotypes suggested their original source was the River Danube. Through analysing the nuclear paralog sequences, evidence was provided of consistent ge...