Scleraetinian was known for its chaotic and difficult morphological identification. DNA barcoding may help for examining such troublesome taxa. The mitochondrial cytochrome oxidase subunit I （CO I ）, mitochondrial 16S and 12S rRNA （mt SSU） genes was always used as standard molecular markers. Here, a total of 21 single individuals of 17 species pertaining to 10 genera of Scleractinian, collected from Xuwen, Guangdong Province, were obtained and combined partial sequences of these three genes, then the base ratio and variations were analyzed using MEGA 5.0. The result indi- cated that the averaged A＋T content of this combined region accounted for 60%, obviously higher than that of G＋C. Also the average Kimura-2-parameter （K2P） distances were conducted. Distance within the same genus was much closer than that of different genu ones. The results showed that the base ratio of Scleractinian mitochondrial gene sequences also obey the rule biased of AT. Well the genetic evolutionary relationship among samples was quantified according to distances analysis. Phylogenetic analysis was carried out with different methods, including neighbor-joining, maximum parsimony and maximum likelihood. The topology of each final trees revealed that molecular systematics is not complete in accor- dance with traditional taxonomy, display classification based on morphological data may be limited by skeleton plasticity. We discuss advantages and disadvantages of the combined sequence as barcodes for scleractinian, and recommend that this marker be considered for scleractinian higher level phylogenetic analysis.%以广东徐闻地区常见的6科10属17种石珊瑚的21个样本为研究对象，对线粒体COI、16SrRNA和mtSSU三基因片段数据进行了联合分析，并计算了属间和科间遗传距离；利用邻接法、最大简约法和最大似然法分别构建了分子系统树。序列分析结果显示，石珊瑚线粒体基因碱基构成同样具有AT偏倚特征；石珊瑚属间的遗传距离显著大于属内遗传距离，而所有石珊瑚与两个外类种群的距离均大于石珊瑚之间的遗传距离；在系统发育树中，分子系统分类结果与形态学分类阐述的遗传进化关系略有差别，暗示传统形态学分类可能受珊瑚骨骼生长可塑性限制。
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