Background: Andes virus (ANDV), part of the Orthohantavirus andesense species, is the principal etiologic agent of hantavirus cardiopulmonary syndrome (HCPS) in southern South America, particularly in Chile and Argentina. The virus is transmitted to humans via aerosolization from excreta of its rodent reservoir, Oligoryzomys longicaudatus. Unlike other hantaviruses, ANDV poses a distinctive public health concern due to its unique capacity for person-to-person transmission. HCPS is characterized by rapid progression to severe respiratory failure and high case-fatality rates. Here, we developed a rapid, amplicon-based Oxford Nanopore sequencing method to generate complete ANDV genomes directly from wild rodents, enhancing genomic surveillance and revealing hidden viral diversity to improve outbreak preparedness in endemic areas. <br><br>Methods: Rodent trapping was conducted between 2011 and 2014 in south-central Chile. Rodents were sero-surveyed for ANDV, and tissues from seropositive mice were further tested using specific ANDV RT-qPCR. RNA from ANDV-positive rodent samples was used to amplify and sequence the complete viral genome. Oxford Nanopore sequencing was performed to generate consensus genomes, and results were validated by resequencing all samples on the Illumina MiSeq platform. Bayesian phylogenetic inference was conducted using new and existing whole ANDV genomes to analyze evolutionary divergence, geographic structure, and selection. <br><br>Findings: Phylogenetic analyses revealed marked evolutionary divergence of ANDV consistent with strong geographic structuring, alongside complex fine-scale phylogeographic intermixing across southern Chile and Argentine Patagonia. Substantial genetic diversity was observed within and between local rodent populations over short spatial and temporal scales, indicating sustained co-circulation of divergent lineages and potential reassortment. Signals of episodic selection were identified, particularly in glycoprotein regions associated with candidate therapeutic antibody recognition sites. <br><br>Interpretation: These results demonstrate the feasibility and value of reservoir-based whole-genome surveillance of ANDV to uncover hidden viral diversity, generating genomic epidemiological data that can inform public health decision-making.