Transposable element activity has greatly impacted the evolution of Kochia scoparia syn. Bassia scoparia (kochia), an important agricultural weed. In this study, an improved kochia genome assembly of the glyphosate-susceptible line 7710 was analyzed in comparison to a glyphosate-resistant line, M32. A near complete genome assembly consisting of 14 pseudochromosomes with a total length of 969.6 Mb, and N50 scaffold length of 99.88 Mb, was generated with hybrid short-read (Illumina), and single-molecule (PacBio/Bionano genomics) data, in addition to chromatin interaction mapping (Hi-C). The 9 largest scaffolds corresponded to the 9 chromosomes of a close relative, Beta vulgaris. From this assembly, 54,387 protein-coding gene loci were annotated. After gene annotation it was revealed that 58% of the whole-genome consisted of transposable elements. We identified that gene families containing FHY3 (FAR-Red Elongated Hypocotyl 3) and FAR1 (FAR-Red Impaired Response 1) functional domains have undergone a massive Bassia-lineage specific expansion. FHY3 and FAR1 domains were first described as a domesticated (non-active) sub-type of Mutator Don-Robertson transposase (MuDR) that function as transcription factors; however, the domains may still function as transposases in the correct genomic context, but this has yet to be observed. Mutator elements are associated with large DNA segmental transposition within the genome including gene duplication events, which can greatly influence plant phenotypes and evolution. We discovered in our work that putative MuDR elements with detectable FHY3/FAR1 domains were tightly associated with segmental duplications of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) that confer resistance to the herbicide glyphosate. Further, in a case study of MuDR activity, we characterized a new MuDR subtype, named here as Muntjac, which contributes to the evolution of herbicide resistance in kochia through the process of transduplication. Collectively, our study provides insights into the de-domestication of a FHY3/FAR1 transposon and provides new perspectives on the evolution of glyphosate resistance in kochia. ### Competing Interest Statement The authors have declared no competing interest.