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Chemical control has become less effective for the invasive weed species horseweed (Conyza canadensis) found in tangerine (Citrus reticulate) orchards of Korea. The dose–response assays of the biotypes of C. canadensiscollected in 2017 from the Jeju province of Korea demonstrated that the amount of glyphosate needed for 50% growth reduction (GR50) in the glyphosate-resistant (GR) biotype was up to 100 times greater than that in the glyphosate-susceptible (GS) biotype (0.328 kg a.e. ha−1). However, the mechanism of resistance in the GR populations of C. canadensisin Korea is unknown. Therefore, this study aimed to determine the mechanism of resistance to glyphosate in the Korean C. canadensispopulations. Shikimic acid accumulation and 5-enolpyruvyl shikimate-3-phosphate synthase(EPSPS) gene expression were analyzed in a GR and a GS biotype of C. canadensis.The GR biotype showed less shikimic acid accumulation than the GS biotype. A target point mutation in the sequence encoding the Pro 106 of EPSPS1was not found after sequencing the GR biotype. Moreover, the expression level of EPSPS1was not altered significantly following application of glyphosate to the GS and GR biotypes, whereas the levels of M10 and M11 ABC transporter genes which play an important role in plant growth and nutrition, and the interaction of the plant with its environment were found to be slightly higher in the glyphosate-treated GS and GR biotypes than the untreated control plants. Our results show that M10 and M11 are likely to be involved in the glyphosate resistance mechanism in C. canadensis. Consequently, non-chemical control methods should be implemented to manage or slow the spread of glyphosate resistance in C. canadensis.