ABSTRACTThe bocachico Prochilodus magdalenae is a freshwater migratory species of great importance for conservation in Colombia. The populations of this fish have been seriously threatened in the last decade, and there is limited knowledge of its genetic conditions.In order to evaluate the genetic structure of P. magdalenae in the Magdalena River basin and some tributaries, the mitochondrial DNA control region was analysed in samples selected from 20 sites.In total, 189 polymorphic sites were detected on a sequence of 500 bp of the control region among 292 individuals, defining 233 haplotypes from which 88.41% were private. Genetic diversity was high (HD = 0.997 and π = 0.0303), neither the analysis of molecular variance, the Φst statistic, nor the Mantel test values revealed significant differences of population subdivision in any of the hierarchical levels. The tests of neutrality and mismatch distribution detected a population expansion in the Middle Pleistocene.Results showed that P. magdalenae forms a large panmictic population in the basin of the Magdalena River. A wide migratory capacity, the absence of geographical barriers and not enough time to accumulate genetic variation are likely reasons for the genetic homogeneity found in this species. Copyright © 2013 John Wiley & Sons, Ltd.