Genomic-based epidemiology can provide insight into the origins and spread of herbicide resistance mechanisms in weeds. We used kochia (Bassia scoparia) populations resistant to the herbicide glyphosate from across western North America to test the alternative hypotheses that 1) a single EPSPS gene duplication event occurred initially in the Central Great Plains and then subsequently spread to all other geographical areas now exhibiting glyphosate-resistant kochia populations or that 2) gene duplication occurred multiple times in independent events in a case of parallel evolution. We used qPCR markers previously developed for measuring the various units of the EPSPS tandem duplication to investigate whether all glyphosate-resistant plants had the same EPSPS repeat structure. We also investigated population structure using simple sequence repeat (SSR) markers to determine the relatedness of kochia populations from across the Central Great Plains, Northern Plains, and the Pacific Northwest. We identified three distinct EPSPS-duplication haplotypes that had geographic associations with the Central Great Plains, Northern Plains, and Pacific Northwest. Population structure revealed a group of populations around the first reported occurrence of glyphosate resistance in the Central Great Plains, a separate group of Pacific Northwest populations, and some relatedness of populations from geographically isolated areas. The results support at least three independent origins of glyphosate resistance in kochia, followed by substantial and mostly geographically localized gene flow to spread the resistance alleles into diverse genetic backgrounds.