Eleusine indica (goosegrass) is a widespread invasive species that poses a significant threat to global agriculture, particularly due to its evolving resistance to glyphosate. While resistance mechanisms such as the Pro106 mutation in the 5-enolpyruvyl-shikimate-3-phosphate synthase (EPSPS) gene are well-characterized, mechanisms can vary significantly by geography. This study investigated the molecular basis of glyphosate resistance in a Korean genotype of E. indica. Unlike genotype reported in other regions, such as Mexico, no Pro106 mutation was detected in the EPSPS gene of the Korean samples. However, Target Site Resistance (TSR) was suggested to be mediated by significant overexpression of EPSPS in glyphosate-treated plants compared to controls. Concurrently, Non-Target Site Resistance (NTSR) mechanisms played a critical role; differential expression analysis revealed the upregulation of key detoxification gene families, including Cytochrome P450s (CYP450), Glutathione S-transferases (GST), and Glycosyltransferases (GT). Furthermore, Gene Ontology (GO) and KEGG pathway analyses indicated a metabolic shift involving the activation of glutathione metabolism and MAPK signaling, coupled with a suppression of photosynthesis-related pathways, suggesting an energy reallocation strategy for survival. These findings demonstrate that glyphosate resistance in Korean E. indica is likely mediated by a complex interplay of EPSPS overexpression and metabolic adaptation, underscoring the importance of understanding regional genetic diversity for developing effective weed management strategies.