Human vaginal microbiome composition is associated with health outcomes such as HIV and STI risk, bacterial vaginosis (BV) and preterm birth. However, genomic diversity and function of many vaginal taxa are poorly understood, and most current knowledge derives from U.S. and European populations. We hypothesized that studying bacteria from a wider range of geographies would offer novel insights into microbial function and approaches to improve vaginal health. We performed comparative genomic analysis of Prevotella bivia – a species linked to BV and HIV risk – in genomes drawn from a catalog of 26,000+ geographically diverse vaginal isolate genomes and culture-independent metagenomes. The analysis revealed that a gene predicted to encode ermF (an rRNA methyltransferase conferring resistance to macrolide antibiotics including clindamycin and azithromycin, which are commonly used to treat BV and STIs) was widely present in North American P. bivia genomes but absent in genomes from a South African cohort. The predicted ermF consistently neighbored a transposase and an uncharacterized outer membrane protein with a beta-barrel domain in P. bivia genomes. Other nearby genes varied among genomes, including predicted resistance genes for tetracyclines (another antibiotic class used for STI treatment), suggesting North American P. bivia strains may have horizontally acquired ermF due to antibiotic pressure. Experimental testing confirmed that ermF-containing North American P. bivia isolates were resistant to clindamycin and azithromycin, while South African isolates lacking ermF were susceptible. Heterologously expressing the predicted ermF gene in E. coli conferred resistance to macrolide antibiotics, confirming the gene’s predicted function and supporting its role in mediating the observed antibiotic resistance in P. bivia. Analysis of other Bacteroidales species within the vaginal bacterial genome catalog revealed that ermF was observed in North American genomes from a diverse range of Prevotella and Bacteroides species, but was not detected in any Prevotella from the South African cohort, including Prevotella disiens – another species linked to adverse cervicovaginal health. These genomic and phenotypic differences across geographical cohorts underscore the importance of broadening vaginal microbiome research to understudied geographies and highlight the need for additional studies of antimicrobial resistance in human vaginal health.