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While Latin America has made significant progress in controlling <jats:italic>Plasmodium falciparum<\/jats:italic>, it faces challenges with residual <jats:italic>P.\u2009vivax<\/jats:italic>. To characterize genetic diversity and population structure and dynamics, we have analyzed the largest collection of <jats:italic>P.\u2009vivax<\/jats:italic> genomes to date, including 1474 high\u2010quality genomes from 31 countries across Asia, Africa, Oceania, and America. While <jats:italic>P.\u2009vivax<\/jats:italic> shows high genetic diversity globally, Latin American isolates form a distinctive population, which is further divided into sub\u2010populations and occasional clonal pockets. Genetic diversity within the continent was associated with the intensity of transmission. Population differentiation exists between Central America and the North Coast of South America, vs. the Amazon Basin, with significant gene flow within the Amazon Basin, but limited connectivity between the Northwest Coast and the Amazon Basin. Shared genomic regions in these parasite populations indicate adaptive evolution, particularly in genes related to DNA replication, RNA processing, invasion, and motility \u2013 crucial for the parasite's survival in diverse environments. 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