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Historically, morphological identification has been the only diagnostic method, but it is inadequate due to morphological similarities between larval stages and limited taxonomic keys. To overcome this, molecular diagnosis is required. However, the DNA sequence information of these neglected parasites remains largely unknown. In this study, pentastomid larvae were collected from the greater omentum of a patient in Northern Thailand. The species of pentastomid larvae was molecularly identified as <jats:italic>Armillifer moniliformis<\/jats:italic>, using PCRs targeting nuclear and mitochondrial regions, followed by Sanger sequencing. Nanopore sequencing was employed to characterize the complete mitochondrial genome of <jats:italic>A. moniliformis<\/jats:italic>, revealing a total length of 16,367\u00a0bp with 37 mitochondrial genes, including 13 protein-coding genes, 22 tRNA genes, and two rRNA genes, as well as one non-coding region. The entire mitogenome is highly AT-rich (62.1%), with nucleotide skews indicating compositional bias between strands. The non-coding region (2616\u00a0bp) lies between the tRNA-Leu<jats:sup>CUN<\/jats:sup> and tRNA-Ser<jats:sup>UCN<\/jats:sup> genes and comprises three repetitive segments. The third repetitive segment is the longest (1659\u00a0bp) and has the highest A\u2009+\u2009T content of 72.2%, likely serving as a regulatory element related to DNA replication. Comparative mitogenome analysis revealed <jats:italic>cox1<\/jats:italic> as the most conserved gene, while <jats:italic>atp6<\/jats:italic>, <jats:italic>atp8<\/jats:italic>, and <jats:italic>nad6<\/jats:italic> exhibit high variability among species. Codon usage analysis indicated that two codon families (Leu1 and Ile) are used more frequently than others, suggesting that these branched-chain hydrophobic amino acids are predominant in transmembrane proteins and underscoring the critical role of the mitochondrion in energy production. Based on single gene (<jats:italic>cox1<\/jats:italic>) and concatenated gene-based phylogenetic approaches, <jats:italic>A. moniliformis<\/jats:italic> clustered closely with other <jats:italic>Armillifer<\/jats:italic> species, with all pentastomids placed taxonomically in the subphylum Crustacea. Mitogenomic phylogenetics in this study demonstrates greater topological precision than <jats:italic>cox1<\/jats:italic> phylogenetics. In conclusion, this study revealed the first complete mitochondrial genome of <jats:italic>A. moniliformis<\/jats:italic>, providing us with novel molecular markers that could effectively facilitate species diagnosis, treatment monitoring, and epidemiological surveillance of pentastomiasis.<\/jats:p>","DOI":"10.1007\/s00436-025-08516-x","type":"journal-article","created":{"date-parts":[[2025,6,27]],"date-time":"2025-06-27T02:07:00Z","timestamp":1750990020000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["First complete mitochondrial genome of Armillifer moniliformis (Pentastomida: Porocephalida) isolated from a human case in Northern Thailand: comparative and phylogenetic analyses"],"prefix":"10.1007","volume":"124","author":[{"given":"Thanapat","family":"Pataradool","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Padet","family":"Siriyasatien","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Woraporn","family":"Sukhumavasi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saruda","family":"Tiwananthagorn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chusana","family":"Suankratay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kanok","family":"Preativatanyou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,6,27]]},"reference":[{"key":"8516_CR1","doi-asserted-by":"publisher","first-page":"W7","DOI":"10.1093\/nar\/gkq291","volume":"38","author":"F Abascal","year":"2010","unstructured":"Abascal F, Zardoya R, Telford MJ (2010) TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. 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