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Historically, the diving duck, Baer’s Pochard ( Aythya baeri ) was widely distributed in East and South Asia, but according to a recent estimate, its global population is now less than 1000 individuals. To date, the mitochondrial genome of  A. baeri  has not been deposited and is not available in GenBank. Therefore, we aimed to sequence the complete mitochondrial genome of this species. The genome was 16,623 bp in length, double stranded, circular in shape, and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one non-coding control region. Many structural and compositional similarities were discovered between  A. baeri  and the other three  Aythya  mitochondrial genomes. Among 13 protein-coding genes of the four  Aythya  species, the fastest-evolving gene was  ATP8  while the slowest-evolving gene was  COII.  Furthermore, the phylogenetic tree of Anatidae based on Bayesian inference and maximum likelihood methods showed that the relationships among 15 genera of the Anatidae family were as follows:  Dendrocygna  was an early diverging lineage that was fairly distant from the other ingroup taxa;  Cygnus ,  Branta , and  Anser  were clustered into one branch that corresponded to the Anserinae subfamily; and  Aythya ,  Asarcornis ,  Netta ,  Anas ,  Mareca ,  Mergus ,  Lophodytes ,  Bucephala ,  Tadorna ,  Cairina , and  Aix  were clustered into another branch that corresponded to the Anatinae subfamily. Our target species and three other  Aythya  species formed a monophyletic group. These results provide new mitogenomic information to support further phylogenetic and taxonomic studies and genetic conservation of Anatidae species.

Mitochondrial genome of the critically endangered Baer’s Pochard, Aythya baeri, and its phylogenetic relationship with other Anatidae species