Chaunocephalus ferox is an intestinal trematode infecting storks and is increasingly recognized as a potential threat to the conservation of the Oriental Stork (Ciconia boyciana). However, its evolutionary history remains poorly understood. In this study, we assembled and annotated the first complete mitochondrial genome of C. ferox using the MITOS2 and GeSeq platforms. The circular genome spans 17,482 bp and encodes 12 protein-coding genes, 22 tRNAs, and 2 rRNAs, with several intergenic overlaps and absence of the atp8 gene. Phylogenetic analyses based on 12 mitochondrial protein-coding genes from 57 trematode species were conducted using maximum likelihood and Bayesian inference methods. While morphological characteristics support its classification within Echinostomatidae, mitochondrial phylogenies yielded inconsistent placements, with C. ferox positioned either near Fasciolidae or outside both families in different gene trees. Divergence time estimation further supports this ambiguity, placing C. ferox's split from other echinostomatids at approximately 75–39 million years ago, a period overlapping with the divergence of Echinostomatidae and Fasciolidae, suggesting it may represent an early-branching lineage. Additionally, cox1 sequences obtained from samples across three regions and two host species were identical, indicating low mitochondrial variation across sampling sites. While the limited sample size precludes firm conclusions about population structure, this pattern may hint at a recent demographic expansion or shared ancestry across geographic areas.
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