[Objective] The research aimed to distinguish Chinese herb Qingjiao from its botanical origin plants by comparing different DNA sequences,so as to provide a molecular basis for origin identification and quality evaluation. [Methods] The cpDNA psbA-trnH and nrDNA ITS sequences of five botanical origin plants from Chinese herb Qingjiao, including Gentiana macrophylla Pall. ,C. straminea Maxim. ,G. crassicaulis Duthie ex Burk. , G. dahurica Fisch snd G. officinalis H. Smith, were amplified with PCR, and then sequenced by direct PCR sequencing method for homologous analysis. [ Results] The length of cpDNA psbA-tmH of five plants was 316 - 318 bp; there were seven different haplotypes and seven variable sites; the GC content of the sequence was 21.2% ; the phylogenetic clustering showed the same as haplotype analysis. The length of nrDNA ITS of five plants was 624 - 625 bp, there were five different hsplotypes and 13 variable sites; the GC conteni of the sequence was 59.3%. The result of phylogenelic clustering suggested that G. dahurica and G. straminea,G. macrophylla and G. officinalis clustered together as sister clade, respectively. [ Conclusion ] The nucleotide differences of nrDNA ITS regions could be used for distinguishing botanical origin in Chinese herb Qingjiao .%[目的]分析奏艽基原植物间不同DNA序列的差异,为秦艽药材DNA条形码的筛选和基原鉴定提供分子证据.[方法]采用PCR扩增纯化后直接测序的方法,测定大叶秦艽(G.macrophylla Pall.)、麻花艽(G.straminea Maxim.)、粗茎秦艽(G.crassicaulis Duthie ex Burk.)、小秦艽(G.dahurica Fisch)、黄管秦艽(G.officinalis H.Smith)5种植物的核糖体DNA ITS、叶绿体DNA psbA-trnH核苷酸序列,并作序列同源性分析.[结果]cpDNA psbA-trnH序列长度变异范围为316～318 bp,有7种不同的单倍型,单倍型间有7个变异位点,序列的GC含量为21.2％；最大简约树的聚类结果与单倍型反映的结果一致.nrDNA ITS序列长度变异范围为624 ～ 625 bp,有5种不同的单倍型,单倍型间有12个变异位点,序列的GC含量为59.3％；最大简约树的聚类结果表明,小秦艽与麻花艽聚为一支,大叶奏艽与黄管秦艽聚为一支,粗茎泰艽位于聚类图的最基部.[结论]nrDNA ITS序列较适合作秦艽基原植物的DNA分子鉴定.
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