Evidence that migration prevents population structure among Neotropical characiform fishes has been reported recently but the effects upon species diversification remain unclear. Migratory species of Prochilodus have complex species boundaries and intrincate taxonomy representing a good model to address such questions. Here, we analyzed 147 specimens through barcode sequences covering all species of Prochilodus across a broad geographic area of South America. Species delimitation and population genetic methods revealed very little genetic divergence among mitochondrial lineages suggesting that extensive gene flow resulted likely from the highly migratory behavior, natural hybridization or recent radiation prevent accumulation of genetic disparity among lineages. Our results clearly delimit eight genetic lineages in which four of them contain a single species and four contain more than one morphologically problematic taxon including a trans-Andean species pair and species of the P. nigricans group. Information about biogeographic distribution of haplotypes presented here might contribute to further research on the population genetics and taxonomy of Prochilodus.

Potamorhina includes the largest species in the Neotropical fish family Curimatidae. They perform long‐distance migrations in large schools and represent relative importance for regional fisheries in South American lowlands. A morphology‐based phylogenetic study recognized five species and proposed interspecific phylogenetic relationships mostly based on osteology, squamation, and morphology of the gasbladder. Subsequent cytogenetic studies revealed extreme variability in diploid numbers and other cytomolecular structures and hypothesized multiple events of chromosome rearrangements with centric fissions followed by reversed fusions. However, neither the taxonomic revision and phylogeny nor the cytogenetic hypothesis of chromosome evolution in Potamorhina was tested using molecular phylogenetic approaches. Here, we use mitochondrial and nuclear DNA sequences to delimit species of Potamorhina with an extensive sampling across the Amazon basin and use phylogenetic methods to test prior hypothesis of multiple events of chromosome rearrangements during the evolution of the genus. Phylogenetic and species delimitation methods clearly support the presence of five species but reveal novel interspecific relationships allowing a reinterpretation of the morphological characters relative to the number of vertebrae, caudal peduncle pigmentation, and modifications in the gasbladder chambers. With the new phylogenetic arrangement, we propose a novel hypothesis of occurrence of a single chromosome fission in the lineage of P. latior followed by an extraordinary event that involved more than 20 chromosome‐pair fissions during the evolution of the ancestor of P. altamazonica and P. squamoralevis. This novel hypothesis represents a simpler and more conceivable explanation for the achievement of these elevated chromosome numbers during the evolution of Potamorhina.