Fine-scale genomic divergence in the Amazonian pirarucu (Arapaima gigas) highlights the need for local management strategies

Freshwater habitats face significant human disturbances globally, impacting food security and ecosystems. Protected areas can mitigate biodiversity loss, but limited data on population connectivity hinders conservation management. This study examines pirarucu ( Arapaima gigas ), a heavily exploited and threatened Amazonian fish, using genomic data to assess fine‐scale genetic structure and its implications for conservation. Samples from 187 pirarucu were collected across 5000 km 2 of várzea floodplain in the Juruá River, Western Brazilian Amazon. Using single nucleotide polymorphism (SNP) data, isolation by distance and genetic population structure were tested. Genetic diversity, contemporary migration and effective population size were estimated. Six intergrading genetic clusters were identified, with stronger genetic separation between lakes upstream and downstream of a main town. Effective population sizes were larger upstream, with migration primarily following river flow. Current genetic differentiation was likely exacerbated by overexploitation near urban areas. These findings emphasise the need for tailored conservation strategies addressing genetic differentiation and overfishing impacts, particularly near towns. Management plans should account for fine‐scale genetic structure to ensure sustainability. We propose protecting one‐third of accessible lakes within 80 km of river sections through Fishing Agreements and better regulating fishing near Carauari to enhance connectivity between lake groups. This research underscores the importance of genetic monitoring and spatial zoning in community‐based conservation efforts for pirarucu and other aquatic vertebrate populations.