Scrophularia takesimensis is a critically endangered endemic species of Ulleung Island, Korea. A previous molecular phylogenetic study based on nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences with very limited sampling suggested that it is most closely related to the clade comprising S. alata and S. grayanoides. To determine the origin of S. takesimensis, we sampled a total of 171 accessions including S. takesimensis (9 populations and 63 individuals) and two closely related species, S. alata (11 populations and 68 individuals) and S. grayanoides (5 populations and 40 individuals) from eastern Asia and sequenced ITS and two chloroplast DNA (cpDNA) non-coding regions. Previously sequenced representative species of Scrophularia (109 taxa for ITS and 80 taxa for cpDNA) were combined with our data set and analyzed. While the global scale ITS phylogenetic tree suggests monophyly for each of the three eastern Asian species, S. takesimensis appears to be more closely related (albeit weakly) to a clade containing eastern North American/Caribbean species than to either S. alata or S. grayanoides. By contrast, the global scale cpDNA phylogenetic tree demonstrates that the eastern North America/Caribbean clade is sister to a clade comprising the three eastern Asian species. In addition, the monophyletic S. takesimensis is deeply embedded within paraphyletic S. alata, sharing its most recent common ancestor with populations from Japan/Sakhalin. Two divergent, geographically structured cp haplotype groups within S. takesimensis suggest at least two independent introductions from different source areas. A new and accurate chromosome number of S. takesimensis (2n = 94) is reported and some conservation strategies are discussed.

玄参（Scrophularia Takeimensis）是韩国Ulleung岛的一种极度濒危的特有物种。先前的基于分子核糖体DNA（nrDNA）内部转录间隔区（ITS）序列的分子系统发育研究仅以非常有限的采样率进行了研究，结果表明，它与包括S. alata和S. grayanoides的进化枝关系最密切。要确定的原点S. takesimensis，我们取样的总的171个种质包括S. takesimensis（9组人群和63个个体）和两个密切相关的物种，S.翅（11群和68个个体）和S. grayanoides（5个种群和40个个体）来自东亚，并对ITS和两个叶绿体DNA（cpDNA）非编码区进行了测序。将先前测序的玄参的代表性物种（ITS的109类和cpDNA的80类）与我们的数据集结合并进行了分析。尽管全球ITS系统发育树表明这三个东亚物种中的每一个都是单系的，但Takesimensis与包含北美东部/加勒比物种的进化枝相比似乎更紧密（尽管微弱），而不是与S.alata或S. Grayanoides。相比之下，全球规模的cpDNA系统发育树表明，北美东部/加勒比进化枝是包含三个东亚物种的进化枝的姊妹。此外，单种的S.takesimensis深深地埋在副生的S. alata中，与日本/萨哈林岛的种群共享其最新的祖先。Takeimensis中的两个地理分布不同的cp单倍型组建议至少两个来自不同来源地区的独立引种。报道了一种新的和精确的S.takesimensis（2n = 94）染色体数目，并讨论了一些保护策略。