The aquatic fern Salvinia molesta D.S. Mitch. is an invasive species that can have devastating effects on the freshwater habitats it colonizes. Currently, a lack of clarity surrounding the genomic composition and genetic diversity of S. molesta impedes eradication efforts. Salvinia molesta is a polyploid hybrid with unknown and controversial parentage, first noted in Africa but morphologically similar to South American species. Giant salvinia is also thought to reproduce primarily, perhaps exclusively, through vegetative reproduction, raising the possibility that the global invasion comprises one or a few clonal genotypes. This research focuses on identifying the maternal genome donor of S. molesta, determining if this species consists of a single or multiple independently derived lineages, and evaluating invasive-range genotypic diversity. Whole chloroplast genome (plastome) sequencing from field-collected and herbarium specimens was used to quantify genetic diversity in S. molesta and the phylogenetic relationships among Salvinia species. Phylogenetic analysis revealed that S. molesta and S. herzogii share the same plastome, although S. herzogii is unlikely to be S. molesta's maternal progenitor due to its own hybrid status and odd ploidy. Rather, we conclude that S. molesta's maternal progenitor is either an undescribed or extinct species. The observed plastome diversity within S. molesta indicates the presence of multiple divergent genotypes which strongly suggest multiple origins of this hybrid. Additionally, this diversity clearly indicates that a single clone does not dominate the invasive range. This genomic diversity could have direct implications for the successful management of this invasive species, particularly for biological control.