It was assumed that closely relative intestinal bacteria hadclosely relative intestinal hosts because of the same or similar symbiosis, vice versa. Based on this assumption, the amount of intestinal bacteria detected in intestines of Cyprinidae fishes was used to analyze the phylogenetic relationship among 8 Cyprinidae fishes: Ctenopharyngodon idellus, Mylopharyngodon piceus, Hypophthalmichthys molitrix, Aristichthys nobilis, Cyprinus carpio haematopterus, Carssius auratus, Megalobrama amblycephala and Megalopbrama terminalis. In the phylogenetic trees, using NJ and UPGMA methods,the genera of each subfamily were joined to a comnon nodal point. Between the subfamilies, Leuciscinae and Culterinae were first joined to a nodal point. The point, which Hypophthalmichthinae and Cyprininae were together joined to, was their ancestral nodal point. The sequence data of the 2 genes cytochrome b and ND4 of mitochondrial genome were also used to analyze the phylogenetic relationship between the 5 subfamilies of Cyprinidae. Both of the phylogenetic trees of cytochrome b and ND4 built by NJ method were different from each other in topological structure. Nevertheless, a common conclusion inferred from the 3 phylogenetic trees is that Cyprinidae is the most primary group and monophyletic in the 5 subfamilies, whereas C.auratus may be the most primary lineage; Culterinae has no position in Cyprinidae phylogenetic tree.%用检测到的肠道微生物菌群的含量对鲤科鱼类的草鱼(Ctenopharyngodon idellus)和青鱼(Mylopharyngodonpiceus)、鲢(Hypophthalmichthys molitrix)和鳙(Aristichthys nobilis)，鲤(Cyprinus carpiohaematopterus)和鲫(Carassius auratus)，团头鲂(Megalobrama amblycephala)和三角鲂(Megalopbrama terminalis)8个种进行系统演化分析。所获得的系统演化树中，每个亚科内的物种邻接为1个接点。在亚科间，雅罗鱼亚科与亚科相邻邻接1个共同接点。该接点与鲢亚科和鲤亚科连结为1个共同祖先接点。用线粒体基因组中的cytb和ND4基因全序列分别构建5个亚科13和11个种的NJ树，这2个树在5个亚科之间的邻接拓扑结构上亦不相同。3种树可推出一个共同的结论是在所分析的亚科中鲤亚科为最原始的类群，而鲫是最原始的类型。
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