We determined the complete sequence of the mitochondrial DNA (mtDNA) of a parasite discovered between the subcutaneous tissue and the peritoneum of an African nocturnal non-human primate (NHP). The parasite and host sequences were obtained by a combination of Sanger sequencing and nanopore MinION techniques. Analyses of mtDNA gene arrangements and sequences unambiguously showed that the parasite investigated was the pentastomid Armillifer armillatus, also commonly named the tongue worm. The full-length mitochondrial genome of A. armillatus, measuring 16,706 bp in length, contains 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, an arrangement identical to that of previously described pentastomid mitochondrial genomes. We describe here the second full mitochondrial genome of A. armillatus to date. To identify the NHP host, maximum likelihood phylogenetic analyses of a 441-bp fragment on the 12S rDNA gene and of a 1,140-bp fragment of the mitochondrial cytochrome b strongly support clustering with the African lorisid Perodicticus potto, a species that has rarely been reported as an intermediate host of this parasite.