This study presents the first genomic evidence of treponemal infections in the Americas before the arrival of Columbus, by analyzing ancient human remains from a 2,000-year-old burial site in Brazil. Four ancient genomes of *Treponema pallidum* were reconstructed, closely related to the *T. pallidum endemicum* subspecies, which causes bejel. These genomes challenge the traditional geographical niche of bejel, which is typically found in arid regions, and highlight the adaptive potential of treponematoses. The high-coverage genome was used to refine molecular clock dating, placing the divergence of modern *T. pallidum* subspecies in pre-Columbian times. The findings suggest that treponemal diseases may have originated earlier and spread more widely than previously thought, with implications for the evolution and spread of *T. pallidum*. The study underscores the value of archaeogenetics in understanding the history and emergence of pathogens.This study presents the first genomic evidence of treponemal infections in the Americas before the arrival of Columbus, by analyzing ancient human remains from a 2,000-year-old burial site in Brazil. Four ancient genomes of *Treponema pallidum* were reconstructed, closely related to the *T. pallidum endemicum* subspecies, which causes bejel. These genomes challenge the traditional geographical niche of bejel, which is typically found in arid regions, and highlight the adaptive potential of treponematoses. The high-coverage genome was used to refine molecular clock dating, placing the divergence of modern *T. pallidum* subspecies in pre-Columbian times. The findings suggest that treponemal diseases may have originated earlier and spread more widely than previously thought, with implications for the evolution and spread of *T. pallidum*. The study underscores the value of archaeogenetics in understanding the history and emergence of pathogens.