Abstract Mitochondrial genome (mtDNA) has advantages in rapid evolution, rich polymorphism and maternally inheritance without gene recombinations, which has become an ideal molecular markers of population genetics, phylogenetics, molecular ecology and taxonomy. In this study, the primers were designed based on the mitochondrial genome sequence of Bean goose (Anser fabalis) which was a closely related species of Swan goose (Anser cygnoides). Swan goose mitochondrial genome sequence was analysed by direct sequencing techniques. The results showed that whole mitochondrial genome sequence was 16 739 bp(GenBank accession No. KJ124555) in Swan goose, including 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes and a D-loop region. Base composition of T, C, A and G were 22.49%, 32.24%, 30.21% and 15.06%, respectively. Besides, the base preference of AT was not determined. 22 kinds of tRNA were all typically cloverleaf structures. Compared to 12SrRNA of Red Junglefowl (Gallus gallus) and Mongolian Ground Jay (Podoces hendersoni), we found the secondary structure of 12SrRNA included 4 domains, 37 stem-loops and 13 salients in the Swan goose, and LSP/HSP, ETAS1-2, goose hairpin, E-box, F-box, D-box, C-box, Bird similarity-box, CSB1-box, CSB-like and OH in the D-loop control region. Finally, taken Red Junglefowl as an outgroup, the phylogenetic tree was constructed based on mitochondrial genome sequences using Neighbor-joining (N-J) algorithm, Maxium-likelihood (ML) algorithm and Bayesian model. The results showed that Swan goose, Greylag goose, Bean goose, white-fronted goose and Canada goose had close genetic relationship. The findings enrich the ducks mitochondrial genome sequences and provide a theoretical basis for the study of geese phylogeny.