Eurasian watermilfoil (Myriophyllum spicatum) can hybridize with the native northern watermilfoil (M. sibiricum) and all three taxa, Eurasian, northern and hybrid watermilfoil are present in Minnesota, but their occurrence and distribution is not well documented. Recent studies elsewhere indicate that some genotypes of hybrid watermilfoil can be tolerant of some auxin-mimic herbicides, leading to concern that treatments with these herbicides could select for genotypes that will be more difficult to control. Using microsatellite markers, we examined the genetic composition of watermilfoils in 2015 in three bays of Lake Minnetonka (Grays, North Arm and St. Albans) that are being managed with auxin-mimic herbicides to control Eurasian watermilfoil. In addition, we examined two bays (Smiths and Veterans) and one lake (Christmas Lake) in 2016 that have not been extensively managed with herbicides. Eurasian, northern and hybrid watermilfoil genotypes were found throughout the study area. However, northern watermilfoil was only found in the untreated water bodies, and at relatively shallower depths compared to pure and hybrid Eurasian watermilfoil. Pure Eurasian watermilfoil was the dominant taxon in all three untreated water bodies. In contrast, hybrid watermilfoil was the dominant taxon in two of the treated water bodies (Grays and North Arm), and was the only watermilfoil found post-treatment in the third water body (St. Albans) despite pure Eurasian watermilfoil being dominant there in June before the herbicide treatment. The apparent association between taxonomic composition and treatment history suggests that intensively managed lakes may be more likely to become dominated by hybrid watermilfoil and less likely to harbor native northern watermilfoil, and this hypothesis warrants further investigation through laboratory and field study. Genetic diversity for all three taxa indicates that sexual reproduction is common. Northern watermilfoil individuals were the most genetically diverse, followed by hybrid watermilfoil, and finally Eurasian watermilfoil. However, we also found clear evidence of extensive clonal reproduction, especially for a few hybrid and Eurasian watermilfoil genotypes that were found in numerous individuals from several water bodies. Water bodies also tended to harbor different genotypes, suggesting that sexual reproduction occurs independently in different water bodies, but that clonal reproduction can lead to extensive spread of specific genotypes within and among water bodies. This allows for the possibility that sexual reproduction generates a diversity of genotypes that may differ in their growth and herbicide response properties, which could facilitate evolutionary dynamics related to the evolution of increased competitive vegetative growth (invasiveness) or herbicide resistance. Our temporal analysis of the three treated bays provides evidence of genetic dynamics that could indicate ongoing evolution of invasiveness and resistance. Of the three treated bays, Grays and St. Albans Bays had a relatively higher degree of herbicidal control compared to North Arm Bay. Although North Arm Bay was dominated by several hybrid genotypes even before treatment, we observed a rapid shift in the genetic composition post-treatment. In particular, we observed a large increase in the proportion of one genotype. It is unclear whether this rapid shift was due to invasive traits such as elevated growth rate or herbicide tolerance, or whether it was due to chance associated with a population bottleneck (reduction in amount of watermilfoil) from the herbicide treatments. Interestingly, the same genotype was the only genotype found in St. Albans Bay post-treatment, and this genotype was not found in pre- or post-treatment samples from Grays Bay, where the herbicide treatments were effective. Taken together, these results identify this genotype as a possible auxin-tolerant and/or faster spreading genotype, and further lab and field studies should explicitly test this hypothesis. Overall, our study highlights some potential benefits of integrating genetic analysis into watermilfoil management projects. Specifically, genotype data can help inform adaptive management planning and evaluation by identifying associations between genetic composition and management history and control actions. In particular, temporal genetic monitoring may identify shifts in composition that may be associated with differences in management-relevant traits such as growth and herbicide response. Genetic analysis can identify specific genotypes of interest that can then be studied explicitly to inform control options, including trigger points for switching specific control techniques.