Species of Centrorhynchus (Polymorphida: Centrorhynchidae) commonly parasitize various falconiform and strigiform birds worldwide. In the present study, the complete mitochondrial (mt) genome sequences of Centrorhynchus clitorideus was sequenced and annotated for the first time based on specimens collected from the little owl Athene noctua (Scopoli) (Strigiformes: Strigidae) in Pakistan. The complete mt genome sequences of C. clitorideus is 15,884 bp in length, and contained 36 genes [two rRNA genes (rrnL and rrnS), 22 tRNA genes and 12 protein-coding genes (PCGs) (lacking atp8)] and two non-coding regions (NCR1 and NCR2), which represents the largest mt genome of acanthocephalan reported so far. In order to assess the systematic position of C. clitorideus and the interrelationship of the family Centrorhynchidae and the other families in order Polymorphida, the phylogenetic tree was constructed using Bayesian inference (BI) based on amino acid sequences of 12 PCGs. Phylogenetic results supported C. clitorideus formed a sister relationship to C. milvus in Centrorhynchidae, which has a sister relationship to the representatives of Polymorphidae + Plagiorhynchidae. Our results revealed the monophyly of Polymorphida and paraphyly of Echinorhynchida in the class Palaeacanthocephala. The validity of the genus Sphaerirostris (Polymorphida: Centrorhynchidae) was also challenged by our phylogenetic results, which seems to be a synonym of Centrorhynchus. Moreover, the present phylogenetic analysis indicated that the family Quadrigyridae and subfamily Pallisentinae (A. cheni and P. celatus) are polyphyletic.

物种Centrorhynchus（Polymorphida：Centrorhynchidae）一般寄生于世界各地的各种falconiform和strigiform鸟类。在本研究中，首次基于从巴基斯坦小猫头鹰雅典娜小夜蛾（Scopoli）（Strigiformes：Strigidae）收集的标本，对阴森森中心线粒体（mt）的完整线粒体基因组序列进行了测序和注释。阴茎线虫的完整mt基因组序列长度为15,884 bp，包含36个基因[两个rRNA基因（rrn L和rrn S），22个tRNA基因和12个蛋白质编码基因（PCG）（缺少atp8）]和两个非编码区（NCR1和NCR2），它们代表了迄今为止报道的棘头动物最大的mt基因组。为了评估阴蒂梭菌的系统位置以及多形目科中斜纹夜蛾科和其他家族的相互关系，基于12个PCG的氨基酸序列，使用贝叶斯推断（BI）构建了系统树。系统发育结果的支持下clitorideus形成的姐妹关系C.鸢属在Centrorhynchidae，其具有到Polymorphidae + Plagiorhynchidae代表的姐妹关系。我们的研究结果揭示了多形纲的单端和棘皮纲的旁系在Palaeacanthocephala类中。鳞球菌属的有效性（Polymorphida：Centrorhynchidae）也受到我们系统发育结果的挑战，这似乎是Centrorhynchus的同义词。此外，目前的系统发育分析表明，四眼纲科和Pal科亚科（A. cheni和P. celatus）是多系统的。