Abstract: The acanthocephalan Hebesoma violentum Van Cleave was collected from the intestine of Siniperca chuatsi Basilewsky, which were captured in the Liangzi Lake of Hubei Province, China. Using long PCR we cloned the entire mitochondrial (mt) genome sequence of H. violentum(13,393 bp) (GenBank accession No. KC415004). The genome consists of 36 genes including 12 protein-coding genes, 22 transfer RNAs (tRNAs) and 2 ribosomal RNAs (rRNAs), which was consistent with previous reports about mt genomes of other acanthocephalan species. All genes in the mt genome were encoded on one strand and transcribed in the same direction. The phylogenetic analysis of the mt genomes of acanthocephalans, rotifers and others indicated that the class Eoacanthocephala, containing Pallisentis celatus Van Cleave, Hebesoma violentum Van Cleave and Paratenuisentis ambiguus Van Cleave, was closely related to Palaeacanthocephala which was then correlated with the class Archiacanthocephala. It is obvious that acanthocephalans are closely related to a clade containing bdelloids which were then correlated with the clade containing monogononts. Further phylogenetic analysis of rotifers in the Seisonidea and acanthocephalans in the Polyacanthocephala will provide insights into the phylogenetic relationship between the major taxa of rotifers and/or acanthocephalans, as well as between these two groups.