Trapa natans, characterized by four-horned fruits, has been recognized as an introduced species in the northeastern United States since the 1920′s. However, in 2014 a two-horned morphotype of Trapa was discovered in the Potomac River in Virginia. As such, we hypothesize the two-horned variety represents a cryptic introduction of a Trapa taxon distinct from the four-horned T. natans previously identified in North America. We tested this hypothesis by genotyping 129 amplified fragment length polymorphism loci for 304 Trapa individuals collected from across the Northeast US and several populations from Asia and Africa. The two-horned and four-horned morphotypes in the northeastern US were found to be genetically and morphologically distinct. The two-horned Trapa taxon was most genetically and morphologically similar to samples from Taiwan identified as T. bispinosa Roxb. var iinumai Nakano. The four-horned Trapa taxon previously identified as T. natans was most genetically and morphologically similar to T. natans collected from Japan, but were genetically distinct. Therefore, it is likely that the US four-horned Trapa was introduced from somewhere outside of Japan, an unsampled area in Japan, or have genetically diverged since introduction. Distinguishing these two US Trapa taxa will be important for documenting spread and identifying new populations, and for further study on the timing and efficacy of physical, chemical, and biological control options. Our study also highlights the need for a comprehensive geographic survey of Trapa morphology and genetics to clarify the taxonomy.