Identifying the origin of invasive plants is an important first step in classical biological control of those plants. However, the historical record is non-specific about the South America origin(s) of the Florida exotic population of Schinus terebinthifolius, Brazilian pepper. To locate the source population(s), we collected Brazilian pepper samples from 345 plants in Florida and 26 plants from Brazil. These samples were genotyped at 8 microsatellite loci, and a region of chloroplast DNA was sequenced. Microsatellite data revealed a significant subdivision within Florida, although genetic diversity was similar across the state. Brazil had a significantly higher allelic richness than Florida. We found two chloroplast haplotypes in Florida and five in Brazil. The more common Florida haplotype was among the Brazilian haplotypes, but the geographic source of the second haplotype has not been identified. Sequence data indicate that the less common Florida haplotype came from a region far from those surveyed in Brazil. In combination, the microsatellite and cpDNA analyses suggest that there were two introductions of Brazilian pepper tree into Florida, with complete mixing of the two types. This suggests that the genotypes found in Florida may be unique, and not found in the native South American range. If that is confirmed to be the case, biological control agents should be sought in the source populations of the two Florida haplotypes.