Fallopia japonica (Japanese knotweed, Polygonaceae) is a well-known East Asian perennial that is established throughout the U.S. and Europe. Another congener, F. sachalinensis, and their hybrid, F. xbohemica, also persist on both continents. Their invasive success is primarily attributed to their ability to spread via clonal growth. However, mounting evidence suggests invasion history and dynamics differ between continents and that sexual reproduction is more common than previously assumed. We used published morphological traits designed to distinguish the three taxa to characterize their distribution in 24 New England towns. We found continuous variation of all five traits, with 84% of our 81 individuals having at least one trait outside parental limits. Hierarchical cluster analysis, along with two chloroplast and one nuclear species-specific markers, suggests the presence of intercrossing, segregating hybrids, and likely introgression between F1 hybrids and F. japonica. Our markers also show the first evidence of bidirectional hybridization between parental taxa in the U.S., emphasizing the complex structure of populations in our region. This study is a first step toward unraveling the evolutionary forces that have made these taxa such aggressive invaders in the U.S. The data may also affect management strategies originally designed for largely monomorphic, clonal populations.