Aythya marilais a large diving duck belonging to the family Anatidae. However, the phylogenetic relationship among theseAythyaspecies remains unclear due to the presence of extensive interspecific hybridization events within theAythyagenus. Here, we sequenced and annotated the complete mitochondrial genome ofA. marila, which contained 22 tRNAs, 13 protein-coding genes (PCGs), 2 ribosomal RNAs, and 1 D-loop, with a length of 16,617 bp. The sizes of the PCGs ranged from 297 to 1824 bp and were all, except forND6, located on the heavy chain (H). ATG and TAA were the most common start and termination codons of the 13 PCGs, respectively. The fastest- and slowest-evolving genes wereATP8andCOI, respectively. Codon usage analysis indicated that CUA, AUC, GCC, UUC, CUC, and ACC were the six most frequent codons. The nucleotide diversity values indicated a high level of genetic diversity inA. marila.FSTanalysis suggested a widespread gene exchange betweenA. baeriandA. nyroca. Moreover, phylogenetic reconstructions using the mitochondrial genomes of all available Anatidae species showed that, in addition toA. marila, four major clades among the Anatidae (Dendrocygninae, Oxyurinae, Anserinae, and Anatinae) were closely related toA. fuligula. Overall, this study provides valuable information on the evolution ofA. marilaand new insights into the phylogeny of Anatidae.