Neotropical rivers contain a diverse assemblage of migratory fishes.  The flannelmouth characin, Prochilodus mariae, migrates seasonally between lowland floodplains of the Orinoco Basin and foothill streams in the Venezuelan Andes.  P. mariae is a heavily exploited fishery species and previous research has shown that its removal can cause dramatic changes in nutrient cycling, community structure, and organic matter dynamics.  Despite its ecological and socioeconomic importance, the migration patterns and population biology of P. mariae are not well understood.  Two complementary techniques were used to explore the origin and movements of Prochilodus that migrate to different streams in the Andes.  We developed microsatellite DNA markers to determine if populations are genetically homogenous or structured.  In addition, we used otolith microchemistry to compare ontogenetic patterns of movement among individuals within and among populations.  These analyses reveal distinctive patterns of natal origin and migration for fish collected at different localities.  Furthermore, individuals within a population appear to be recruited from multiple natal sites.  The integration of these techniques is unique for Neotropical fishes and these results have important implications for the conservation and management of this critical species.