外來植物的入侵及歸化，常造成棲地生物多樣性之失衡，也可能影響人畜的健康，或關聯於進出口農產品貿易及國際利益等因素。因此如何建立正確、快速及靈敏的檢測方法，為杜防有害外來植物入侵的重要植物防檢疫工作。南美獨行菜(Lepidium bonariense L.)為十字花科(Brassicaceae)獨行菜屬一年生草本植物，原產地位於南美洲，現已成為臺灣中部非耕地的新歸化雜草。由於南美獨行菜與獨行菜(L. virginicum L.)的植株及種子外觀極為相似，易造成形態鑑定上的困擾。分子標誌己普遍運用於植物種類之鑑別，本研究以簡單序列重複區間(Inter-SimpleSequence Repeat, ISSR)及隨機增幅片段多型性(Random Amplified PolymorphicDNA, RAPD)分子標誌技術，針對南美獨行菜與獨行菜葉片中基因組核酸之差異，篩選出ISSR 編號為UBC807、818、820、823、846、849、855、873 及881 等9個引子，可於南美獨行菜與獨行菜分別增幅300-3,000 bp 之間的2 至7 條多型性核酸條帶；亦篩選出RAPD 編號為4、16、17、23、25、30、31 及50 等8 個引子，可分別增幅400-2,000 bp 之間的2 至8 條多型性核酸條帶。再以可明顯區別此2植物的ISSR UBC820、823、846、849 等4 個引子及RAPD 16、17 及31 等3 個引子進行南美獨行菜與獨行菜種子之檢測，僅需50 ng DNA 為模板，皆可增幅出與葉片相同長度的主要核酸，具顯著區別南美獨行菜及獨行菜之效果，後續可應用於進口作物種子中夾帶雜草種子之檢驗，或入侵來源比對之用，協助外來入侵植物風險評估之舉證。

Invasion by alien species represents one of the greatest biological threats tobiodiversity, second only to habitat destruction. In addition to affecting ecosystems andcontributing to the extinction of native species, invasive alien species also cause majorsocio-economic damage and may affect human and animal health. Thus developingaccurate, fast and sensitive methods to detect harmful exotic plants is one of the mostimportant projects of plant inspection and quarantine works. Lepidium bonariense L., anannual Brassicaceae plant native to South America, has become an naturalized plant inTaiwan in recent decades. As the morphological characteristics are similar, L. bonariense L.has been easily misidentified with L. virginicum L. DNA-based molecular markers havebeen used to detect the genetic diversity of invaded alien species. Novel methods for theidentification of L. bonariense and L. virginicum at the early stage of plant developmentbased on Inter-Simple Sequence Repeat (ISSR) and Random Amplified Polymorphic DNA(RAPD) markers in this study. The results of ISSR and RAPD analysis, only #820, 823,846, 849 ISSR UBC primers and # 16, 17, 31 RAPD primers could significantly distinguishL. bonariense and L. virginicum by 2-7 and/or 2-8 different polymorphic markers. Theseresults indicated that ISSR and RAPD methods can rapid, accurate identification of L.bonariense and may assist the effective management of this invasive species to maintain thebalance of biodiversity in agricultural ecosystems.