Population genetic studies of within- and among-population genetic variability are still lacking for managed submerged aquatic plant species, and such studies could provide important information for managers. For example, the extent of within-population genetic variation may influence the potential for managed populations to locally adapt to environmental conditions and control tactics. Similarly, among-population variation may influence whether specific control tactics work equally effectively in different locations. In the case of invasive Eurasian watermilfoil (Myriophyllum spicatum L.), including interspecific hybrids with native northern watermilfoil (Myriophyllum sibiricum Kom.), managers recognize that there is genetic variation for growth and herbicide response. However, it is unclear how much overall genetic variation there is, and how it is structured within and among populations. Here, we studied patterns of within- and among-lake genetic variation in 41 lakes in Michigan and 62 lakes in Minnesota using microsatellite markers. We found that within-lake genetic diversity was generally low, and among-lake genetic diversity was relatively high. However, some lakes were genetically diverse, and some genotypes were shared across multiple lakes. For genetically diverse lakes, managers should explicitly recognize the potential for genotypes to differ in control response and should account for this in monitoring and efficacy evaluation and using pretreatment herbicide screens to predict efficacy. Similarly, managers should consider differences in genetic composition among lakes as a source of variation in the growth and herbicide response of lakes with similar control tactics. Finally, laboratory or field information on control efficacy from one lake may be applied to other lakes where genotypes are shared among lakes.