Morphological characteristics of the acanthocephalan Polymorphus minutus (Goeze, 1782), which was collected from the duck Anas platyrhynchos Linnaeus in the Czech Republic, are described. The mitochondrial (mt) genome of P. minutus was sequenced, with a total length of 14,149 bp, comprising 36 genes including 12 protein coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA genes (rrnL and rrnS). This genome is similar to the mt genomes of other syndermatan species. All these genes were encoded on the same DNA strand and in the same orientation. The overall nucleotide composition of the P. minutus mt genome was 38.2% T, 27.3% G, 26.2% A, and 8.3% C. The amino acid sequences of 12 PCGs for mt genomes of 28 platyzoans, including P. minutus, were used for phylogenetic analysis, and the resulting topology recovers P. minutus as sister to Southwellina hispida (Van Cleave, 1925), and the two taxa form a sister clade to Centrorhynchus aluconis (Müller, 1780) and Plagiorhynchus transversus (Rudolphi, 1819), which are all species in the Palaeacanthocephala, thus supporting the monophyly of this class.