The mitogenome of Brentisentis yangtzensis is 13,864 bp in length and has the circular structure typical of metazoans. It contains 36 genes: 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and 12 protein-encoding genes (PCGs). All genes are transcribed from the same strand. Thirteen overlapping regions were found in the mitochondrial genome. The overall A+T content of B. yangtzensis is 68.3% versus 31.7% of G+C content (A = 27.8%, T = 40.5%, C = 9.0%, G = 22.7%). B. yangtzenensis (Illiosentidae) and Leptorhynchoides thecatus (Rhadinorhynchidae) form a sister Glade, showing the relatively close relationship between the Illiosentidae and the Rhadinorhynchidae. The mitochondrial gene arrangements of acanthocephalan species are relatively conserved, with only a few translocations of tRNAs (trnS1, trnS2, trnV, and trnK) detected. An identical gene order was found both in a sister Glade (Centrorhynchus aluconis and Plagiorhynchus transversus) and across different classes (B. yangtzensis (Palaeacanthocephala), Acanthosentis cheni (Eoacanthocephala) and Marnzcanthorhynchus hirudinaceus(Archiaca nthocephala), Oncicola luehei and L. thecatus (Palaeacanthocephala)). More studies and more sequences of acanthocephalan species are needed to gain a clear understanding of the phylogenetic relationships.