根據臺灣植物誌之記載鬼針草(Bidens pilosa L.)於臺灣地區共有三個變種，分別為大花咸豐草(B. pilosa var. radiata)、小白花鬼針(B. pilosa var. minor)及白花鬼針(B. pilosa var. pilosa)。本研究採集此三個變種共11個族群161株個體，加上7株當控制組的鬼針舅(Bidens biternata)共168個樣本，分別進?ITS1、 5.8S及ITS2等三個細胞核核?體DNA (nrDNA)的基因位與trnL intron及trnL-trnF IGS等?個??體(cpDNA)的基因位之序?分析，將nrDNA之三個基因位及cpDNA之?個基因位之序?分別合併再進?排比後其序?長?分別為637及799 bp，本研究即以此排比後之nrDNA及cpDNA序?進?此三個變種間、變種內、族群間及族群內等?同階層之遺傳多樣性及基因交?之探討。根據核?酸變?位點(S)、序?型(H)、基因型歧??(gene diversity，Hd)、核?酸歧??(nucleotide diversity，π)、遺傳歧??（genetic diversity，θ）等相關指?顯示nrDNA其遺傳多樣性均遠高於cpDNA。至於族群內及變種內之遺傳分化程?(FST)為大花咸豐草＜小白花鬼針＜白花鬼針，而基因交?值(Nm)則反之（大花咸豐草＞小白花鬼針＞白花鬼針）。AMOVA分析之結果顯示Bidens pilosa遺傳變?的主要貢獻為族群內個體間的變?，於nrDNA及cpDNA均佔50 ％以上，其次則為變種間及變種內族群間的遺傳變?所致。大花咸豐草與其他?變種間的基因交?程?遠低於白花鬼針與小白花鬼針之間的基因交?值，極可能較早歸化的白花鬼針與小白花鬼針間已出現明顯的雜交現象，至於較晚歸化的大花咸豐草與此二變種間的雜交現象則可能尚?明顯。

According to the Flora of Taiwan, there are three varieties of Bidens pilosa L. They are var. radiata, var. minor and var. pilosa. To discover the genetic diversity and gene flow in different hierarchy (inter-varieties, intra-varieties, inter-populations and intra-populations) in these varieties, this study investigated 161 samples from these varieties comprising 11 different populations and 7 samples of Bidens biternata for out-group control. The internal transcribed spacer (ITS1 and ITS2) and the 5.8S of nuclear ribosomal DNA (nrDNA), trnL intron and trnL-trnF IGS loci of the chloroplast genome were amplified and sequenced in all samples. For further analysis, the sequences of ITS1, ITS2 and 5.8S were combined and aligned as nrDNA sequence which covered 637 bp. And the sequences of trnL intron and trnL-trnF IGS were combined as cpDNA with 799 bp alignment. It showed that the genetic diversity of nrDNA sequence was higher than that of cpDNA from the data of the number of polymorphic sites (S), number of haplotypes (H), gene diversity (Hd), nucleotide diversity (π) and genetic diversity (θ). The genetic distances (FST) of intra-populations and intra-varieties was with the following order, var. radiata ＜ var. minor ＜ var. pilosa, and the gene flow (Nm) has shown var. radiata ＞ var. minor ＞ var. pilosa. From the results of the analysis of molecular variance (AMOVA), there are more than 50 % variance contributed by the variance of