The evolution of herbicide resistance is a fascinating example of contemporary evolution, and provides opportunities to study the genetics and genomics of adaptation. In addition, identifying the genetic architecture of resistance has practical value for developing tools for nuisance plant management (e.g., genetic tests for herbicide susceptibility versus resistance). Although much attention has been paid to the genetics and genomics of herbicide resistance in terrestrial weeds of agricultural significance, comparatively little attention has been paid to invasive aquatic plants, which are also frequently managed with herbicides. Here, we focus on the genetic architecture of herbicide resistance in the invasive aquatic plant, Eurasian watermilfoil (Myriophyllum spicatum L). We developed a genetic mapping population for fluridone resistance by crossing a known resistant strain to a known susceptible strain. We identified resistant versus susceptible progeny from this cross by exposing them to 6 ppb fluridone for several weeks. Then, we performed whole-genome sequencing on the most resistant (‘resistant bulk’) and most susceptible (‘susceptible bulk’) progeny to compare DNA sequence variant frequencies across the genome between the two bulks. We identified a large-effect quantitative trait locus (QTL). Interestingly, the gene for the phytoene desaturase enzyme (PDS) – the molecular target for fluridone – is not located on this chromosomal region. This indicates that structural mutation in the phytoene desaturase enzyme is not the mechanism of resistance for this strain. Further, comparison of PDS expression in susceptible versus resistant strains suggests that resistance is not related to increased PDS expression. Taken together, these results suggest that fluridone resistance in this strain is non-target site resistance (e.g., metabolism, reduced uptake or translocation). Current research focuses on 1) identifying the causal variant(s) for fluridone resistance in this population, 2) developing a molecular test for resistance in this population, and 3) comparing QTL from a second fluridone resistance mapping population to study repeatability of herbicide resistance mechanisms.