Anabarilius duoyiheensis
is a native and rare fish in Yunnan. In this study, the complete mitochondrial genome of
A. duoyiheensis
was sequenced and published for a total of 16,614 bp, including 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and one control region. The phylogenetic analysis based on the complete mitochondrial genome showed that
A. duoyiheensis
belongs to the clade of the genus
Anabarilius
and was sister to the clade of
Hemiculter
. This study also contributes to the genus phylogeny of
Anabarilius
and other members of the family Xenocyprididae.