Damming shapes genetic patterns and may affect the persistence of freshwater fish populations

River damming threatens freshwater biodiversity worldwide by isolating populations, reducing both gene flow and genetic variation, and affecting the ability of a given population to adapt to environmental changes. Herein, we employed a microsatellite DNA marker panel and a multitemporal approach to assess the effects of damming on the genetic diversity of a long-lived species from both contemporary and historical perspectives. To accomplish this, we used the migratory catfish Pseudoplatystoma corruscans as a model and sampled it in two South American basins. We tested whether: (1) populations from dammed and undammed environments would display different levels of genetic diversity; (2) ecosystem size would influence the level of genetic diversity; and (3) projected whether fish populations would maintain their current genetic diversity in the long term. Our findings reveal that P. corruscans populations from dammed landscapes with smaller ecosystems showed smaller estimated effective population size, lower genetic diversity, and higher relatedness coefficient than in intermediate ecosystem size in both dammed and undammed environments. We also noticed changes in estimated gene flow and effective population size from both contemporary and historical perspectives, probably because of dams. Predictive genetic diversity analysis revealed a critical scenario for the long-term persistence of P. corruscans in dammed environments with smaller ecosystem sizes. Our study suggests that anthropogenic barriers have substantially impacted genetic diversity and genetic structuring of the migratory fish P. corruscans. Thus, the formation of conservation policies is urgently needed to avoid local extinctions of this species in fragmented riverscapes. We highlighted the effectiveness of large ecosystems and connectivity between populations in conserving genetic diversity of migratory fishes.