中文摘要：

被子植物系统发育学是研究被子植物及其各类群间亲缘关系与进化历史的学科。从20世纪90年代起，核苷酸和氨基酸序列等分子数据开始被广泛运用于被子植物系统发育研究，经过20多年的发展，从使用单个或联合少数几个细胞器基因，到近期应用整个叶绿体基因组来重建被子植物的系统发育关系，目、科水平上的被子植物系统发育框架已被广泛接受。在这个框架中，基部类群、主要的5个分支（即真双子叶植物、单子叶植物、木兰类、金粟兰目和金鱼藻目）、每个分支所包含的目以及几个大分支包括的核心类群等都具有高度支持。与此同时，细胞器基因还存在一些固有的问题，例如单亲遗传、系统发育信息量有限等，因此近年来双亲遗传的核基因在被子植物系统发育研究中的重要性逐渐得到关注，并在不同分类阶元的研究中都取得了一定进展。但是，被子植物系统发育中仍然存在一些难以确定的关系，例如被子植物5个分支之间的关系、真双子叶植物内部某些类群的位置等。本文简述了20多年来被子植物系统发育深层关系的主要研究进展，讨论了被子植物系统发育学常用的细胞器基因和核基因的选用，已经确定和尚未确定系统发育位置的主要类群，以及研究中尚存在的问题和可能的解决方法。

英文摘要：

Angiosperm phylogenetics investigates the evolutionary history and relationships of angiosperms based on the construction of phylogenetic trees. Since the 1990s, nucleotide or amino acid sequences have been widely used for this and angiosperm phylogenetic analysis has advanced from using single or a combination of a few organellar genes to whole plastid genome sequences, resulting in the widely accepted modern molecular systematics of angiosperms. The current framework of the angiosperm phylogeny includes highly supported basal angiosperm relationships, five major clades （eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales）, orders grouped within these clades, and core groups in the monocots or eudicots. However, organellar genes have some limitations; these involve uniparental inheritance in most instances and a relatively low percentage of phylogenetic informative sites. Thus, they are unable to resolve some relation- ships even when whole plastid genome sequences are used. Therefore, the utility of biparentally inherited nu- clear genes with more information about evolutionary history, has gradually received more attention. Nevertheless, there are still some plant groups that are difficult to place in the angiosperm phylogeny, such as those involving the relative positions of the five major groups as well as those of several orders of eudicots. In this review, we discuss the applications, advantages and disadvantages of marker genes, the deep relationships that have been resolved in angiosperm phylogeny, groups with uncertain positions, and the challenges that remain in resolving an accurate phylogeny for angiosperms.