Life‐History and Landscape Context Shaping the Spatial Genetic Structure of the Migratory Amazonian Fish Prochilodus nigricans

The Neotropical migratory fish Prochilodus nigricans plays a critical ecological and socioeconomic role in the Amazon basin. Nevertheless, little is known about its populations and the genetic diversity pattern of the species. In light of this, the current study investigates the spatial genetic structure and diversity of P. nigricans populations in the Tapajós River basin, focusing on the Juruena and Teles Pires River sub‐basins, before the widespread development of hydroelectric plants planned in the region. Using mitochondrial (ATP6/8 and D‐loop) markers and eight microsatellite loci, we analysed 239 individuals from nine collection sites. Significant genetic differentiation between the Juruena and Teles Pires sub‐basins, with mitochondrial data identifying four genetic groups: Juruena, Teles Pires, Apiacás and Tapajós. Microsatellite analyses identified two main genetic clusters: Juruena and Teles Pires‐Tapajos group. D‐loop data exhibited high haplotype diversity, particularly in the Teles Pires population, whereas microsatellites indicated moderate overall genetic diversity. Genetic differentiation among populations was explained by riverscape distance, with other natural barriers (rapids and waterfalls) likely further contributing to the observed patterns of genetic structure. Our study provides new insights into factors shaping population structure patterns and highlights the species' adaptability to localised flood‐pulse systems, contrasting with the extensive migrations of subtemperate congeneric species. Therefore, it is essential to preserve the upper reaches of the basins, which support different populations capable of completing their life cycle, largely due to the presence of marginal lagoons that provide critical breeding and nursery habitats. We highlight that hydropower dams planned for this region represent threats by altering these ecosystems and compromising genetic diversity.