Variable milfoil, Myriophyllum heterophyllum, has become a major management concern in the northeastern US owing to its apparently recent invasion into, and nuisance growth in, these states where it is not considered native historically.  Despite increasing attention from lake managers, very little is known about the historical biogeography, ecology, or genetics of variable milfoil.  In fact, even its current geographic distribution is not fully understood because of extensive taxonomic confusion among milfoil species.  We present results from a genetic survey of M. heterophyllum from across North America using nuclear and chloroplast DNA sequences and polymorphic microsatellite markers.  We find surprising phylogeographic structure, even across portions of its ‘introduced’ range in the northeastern US.  We discuss the implications of its current phylogeographic patterning with respect to alternative biogeographic hypotheses for its spread to the northeastern US.  In addition, we find surprising genetic diversity among invasive lineages in Maine that are morphologically indistinguishable in the field.  A subsequent greenhouse common garden growth study revealed clear morphological differences among genetically distinct lineages.  We discuss the implications of this cryptic diversity for understanding pattern and process in this biological invasion, and we describe how our phylogeographic study can inform critical field experiments.  We present alternative hypotheses for discordance among observed phylogenetic relationships for nuclear versus chloroplast DNA sequences among our samples, and discuss their management implications.  We advocate this system as a promising model for studying the ecological genetics of biological invasions.