The Western equine encephalitis virus is transmitted between mosquitoes and wild birds. Mosquitoes spread the virus to horses and human populations, causing severe encephalitis and death. The most recent large outbreak occurred in South America from November 2023 to April 2024. We identified and genetically characterized Uruguayan strains during this outbreak to understand their evolutionary trends and rapid expansion. We obtained genomes from 15 strains using a novel multiplex PCR assay combined with next-generation Illumina sequencing. The phylogenetic analysis revealed that viruses from Uruguay and Brazil collected during the outbreak and an Argentine strain from 1958 share a common evolutionary origin and are distinct from North American strains. Phylogenetic and epidemiological data suggest that the outbreak originated in Argentina and spread to Uruguay and Brazil, likely by movements of infected birds. Genomic analysis also revealed mispairing in real-time PCR primers and probes that may affect official diagnostic protocols.